April 17, 2015
Bioconductors:
We are pleased to announce Bioconductor 3.1, consisting of 1024 software packages, 241 experiment data packages, and 917 up-to-date annotation packages.
There are 95 new software packages, and many updates and improvements to existing packages; Bioconductor 3.1 is compatible with R 3.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Amazon Machine Image and Docker containers.
Visit for details and downloads.
To update to or install Bioconductor 3.1:
Install R 3.2. Bioconductor 3.1 has been designed expressly for this version of R.
Follow the instructions at.
There are 95 new packages in this release of Bioconductor.
AIMS - This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.
AnalysisPageServer - AnalysisPageServer is a modular system that enables sharing of customizable R analyses via the web.
bamsignals - This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.
BEclear - Provides some functions to detect and correct for batch effects in DNA methylation data. The core function “BEclear” is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.
bir.
BrowserViz - Interactvive graphics in a web browser from R, using websockets and JSON
BrowserVizDemo - A BrowserViz subclassing example, xy plotting in the browser using d3
BubbleTree - BubbleTree utilizes homogenous pertinent somatic copy number alterations (SCNAs) as markers of tumor clones to extract estimates of tumor ploidy, purity and clonality.
canceR -).
CAnD - Functions to perform the non-parametric and parametric CAnD tests.
Cardinal - Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
chromDraw - Package chromDraw is a simple package for linear and circular type of karyotype visualization. The linear type of visualization is usually used for demonstrating chromosomes structures in karyotype and the circular type of visualization is used for comparing of karyotypes between each other. This tool has own input data format or genomicRanges structure can be used as input. Each chromosome containing definition of blocks and centromere position. Output file formats are *.eps and *.svg.
Clonality - Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles
CODEX -.
cogena - Description: Gene set enrichment analysis is a valuable tool for the study of molecular mechanisms that underpin complex biological traits. As the method is conventionally used on entire omic datasets, such as transcriptomes, it may be dominated by pathways and processes that are substantially represented in a dataset, however the approach may overlook smaller scale, but highly correlated cellular events that may be of great biological relevance. In order to detect these discrete molecular triggers, we developed a tool, co-expressed gene-set enrichment analysis (cogena), for clustering differentially expressed genes and identification of highly correlated molecular expression clusters. Cogena offers the user a range of clustering methods, including hierarchical clustering, model based clustering and self-organised mapping, based on different distance metrics like correlation and mutual information. After obtaining and visualising clusters, cogena performs gene set enrichment. These gene sets can be sourced from the Molecular Signatures Database (MSigDB) or user-defined gene sets. By performing gene set enrichment across expression clusters, we find considerable enhancement in the resolution of molecular signatures in omic data at the cluster level compared to the whole.
coMET -.
ComplexHeatmap - Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential features. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.
conumee - This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k methylation arrays.
CopywriteR - CopywriteR generate DNA copy number profiles from whole exome sequencing by analysing the offtarget sequence reads. By exploiting the offtarget sequence reads, it allows for creation of robust copy number profiles from WES with a uniform read depth and evenly distributed data points over the genome.
cpvSNP -.
cytofkit - An integrated mass cytometry data analysis pipeline that enables simultaneous illustration of cellular diversity and progression.
diffHic - Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.
diggit - Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm
DMRcaller -.
edge -.
EMDomics - The EMDomics algorithm is used to perform a supervised two-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between two two distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover’s Distance (EMD) algorithm instead computes the “work” needed to transform one distribution into the other, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores.
ENCODExplorer - This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.
ENmix - Illumina HumanMethylation450 BeadChip has a complex array design, and the measurement is subject to experimental variations. The ENmix R package provides tools for low level data preprocessing to improve data quality. It incorporates a model based background correction method ENmix, and functions for inter-array quantile normalization, data quality checking, exploration of multimodally distributed CpGs and source of data variation. To support large scale data analysis, the package also provides multi-processor parallel computing wrappers for some commonly used data preprocessing methods, such as BMIQ probe design type bias correction and ComBat batch effect correction.
ensembldb -.
FISHalyseR - FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.
FlowRepositoryR - This package provides an interface to search and download data and annotations from FlowRepository (flowrepository.org). It uses the FlowRepository programming interface to communicate with a FlowRepository server.
FlowSOM - FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees
flowVS - Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.
gdsfmt - This, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are also supported with relatively efficient random access. It is allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.
GENESIS - The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015): a Principal Components Analysis with genome-wide SNP genotype data for robust population structure inference in samples with related individuals (known or cryptic).
genom.
gespeR - Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.
ggtree - ggtree extends the ggplot2 plotting system which implemented the grammar of graphics. ggtree is designed for visualizing phylogenetic tree and different types of associated annotation data.
GoogleGenomics - Provides an R package to interact with the Google Genomics API.
gQTLBase - Infrastructure for eQTL, mQTL and similar studies.
gQTLstats - computationally efficient analysis of eQTL, mQTL, dsQTL, etc.
GreyListChIP - Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.
gtrellis - Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and add self-defined graphics in the plot.
HIBAG -.
immunoClust - Model based clustering and meta-clustering of Flow Cytometry Data
InPAS - Alternative polyadenylation (APA) is one of the important post-transcriptional regulation mechanism which occurs in most human genes. InPAS, developed form DaPars algorithm, predicts and estimates APA and cleavage sites for mRNA-seq data. It uses the power of cleanUpdTSeq to adjust cleavage sites.
IVAS - Identification of genetic variants affecting alternative splicing.
LEA -.
LowMACA -.
mAPKL - We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes.
MatrixRider - Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.
mdgsa - Functions to preform a Gene Set Analysis in several genomic dimensions. Including methods for miRNAs.
MeSHSim - Provide for measuring semantic similarity over MeSH headings and MEDLINE documents
MethTargetedNGS - Perform step by step methylation analysis of Next Generation Sequencing data.
mogsa - This package provide a method for doing gene set analysis based on multiple omics data.
msa - This.
muscle - MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.
NanoStringQCPro -.
netbenchmark - This package implements a benchmarking of several gene network inference algorithms from gene expression data.
nethet - Package).
OmicsMarkeR - Tools for classification and feature selection for ‘omics’ level datasets. It is a tool to provide multiple multivariate classification and feature selection techniques complete with multiple stability metrics and aggregation techniques. It is primarily designed for analysis of metabolomics datasets but potentially extendable to proteomics and transcriptomics applications.
pandaR - Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complimentary data sources.
parglms - support for parallelized estimation of GLMs/GEEs, catering for dispersed data
pmm -.
podkat -.
PROPER - This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.
ProtGenerics - S4 generic functions needed by Bioconductor proteomics packages.
pwOmics - pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and proteins. A separate downstream analysis of proteomic data including pathway identification and enrichment analysis, transcription factor identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream transcription factors and regulators. The cross-platform comparative analysis allows for comprehensive analysis of single time point experiments and time-series experiments by providing static and dynamic analysis tools for data integration.
QuartPAC - Identifies clustering of somatic mutations in proteins over the entire quaternary structure.
R3CPET - The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.
RBM - Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.
rcellminer - () has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.
RCyjs - Interactvive viewing and exploration of graphs, connecting R to Cytoscape.js
regioneR - regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.
rGREAT - This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user’s input and automatically retrieving results from GREAT web server.
rgsepd -.
Rhtslib - This package provides version 1.1 of the ‘H”).
RNAprobR - This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.
RnaSeqSampleSize - RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data
RnBeads - RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
RUVcorr - RUVcorr allows to apply global removal of unwanted variation (ridged version) to real and simulated gene expression data.
saps -.
SELEX - Tools for quantifying DNA binding specificities based on SELEX-seq data
seq2pathway -.
seqPattern - Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.
sigsquared - By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.
SIMAT -.
similaRpeak - This package calculates metrics which assign a level of similarity between ChIP-Seq profiles.
sincell -.
skewr - The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the “rs” SNP probes and the probes associated with imprinted genes as series of ‘tick’ marks located above the x-axis.
soGGi -.
SVM2CRM - Detection of cis-regulatory elements using svm implemented in LiblineaR.
TIN -.
TPP - Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).
TRONCO -.
Package maintainers can add NEWS files describing changes to their packages since the last release. The following package NEWS is available:
Changes in version 1.39.4 (2015-01-18):
ROBUSTNESS: ‘GNU make’ is a SystemRequirements (for now).
ROBUSTNESS: Did not seem to be needed, but package is now a good citizen and do library.dynlib.unload() when unloaded.
CLEANUP: Now using requireNamespace() instead of require().
CLEANUP: Internal cleanup of native code.
Changes in version 1.39.3 (2014-11-26):
Changes in version 1.39.2 (2014-10-28):
BUG FIX: The range test of argument ‘units’ to readCdf() and readCdfQc() was never performed due to a typo, meaning it was possible to request units out of range. Depending on system this could result in either a core dump or random garbage read for the out of range units.
ROBUSTNESS: Added package system tests for out of range ‘units’ and ‘indices’ arguments for most read functions.
Changes in version 1.39.1 (2014-10-26):
ROBUSTNESS: Now all methods gives an informative error message if zero elements are requested, i.e. via zero-length argument ‘indices’ or ‘units’ that is not NULL. Previously this case would access all values just like NULL does.
ROBUSTNESS: Now readCelRectangle() gives an informative error message if argument ‘xrange’ or ‘yrange’ is not of length two.
BUG FIX: readPgf() and readPgfEnv() would give an error if argument ‘indices’ was specifies as a double rather than as an integer vector.
Changes in version 1.39.0 (2014-10-13):
Changes in version 1.6.0:
NEW FEATURES
ASEset slot for Phase information
generation of masked reference genomes
calculation of reference fraction ‘refFraction’
Changes in version 0.99.5:
First release to Bioconductor
See AnalysisPageServer vignette for introduction.
Changes in version 1.30:
NEW FEATURES and API changes
Adds mapIds() which allows users who miss mget() to extract data from AnnnotationDb objects: but without the dangers of using mget() (which fails if you pass in a bad key)
Adds dbconn() and dbfile() methods to the list of things that AnnotationDb derived objects shoould always be expected to support
BUG FIXES AND CODE MAINTENANCE
Changes in version 2.0.0:
NEW FEATURES and API changes
AnnotationHub is all new. We basically rewrote the entire thing.
The back end is new (new database, new way of tracking/routing data etc.)
The front end is new (new AnnotationHub object, new methods, new behaviors, new ways of finding and downloading data)
The metadata has also been cleaned up and made more consistent/searchable
The recipes that are used to populate these data have also been cleaned up.
There is also a new vignette to explain how to use the new AnnotationHub in detail
Improvements since last time
The old way of finding data (an enormous tree of paths), was not really scalable to the amount of data we have to provide access to. So we junked it. Now you have a number of better methods to allow you to search for terms instead.
The new hub interface can be searched using a new display method, but it can also be searched entirely from the command line. This allows you to use it in examples and scripts in a way that is friendlier for reproducible research.
For users who want to contribute valuable new annotation resources to the AnnotationHub, it is now possible to write a recipe and test that it works for yourself. Then once you are happy with it, you can contact us and we can add data to the AnnotationHub.
Changes in version 2.3.3 (2015-02-18):
Changes in version 2.3.2 (2015-02-17):
ROBUSTNESS: Added package tests. Code coverage is 76%.
CLEANUP: Using requestNamespace() instead of request().
Changes in version 2.3.1 (2014-12-08):
Changes in version 2.3.0 (2014-10-13):
Changes in version 2.2.1 (2014-12-08):
Changes in version 1.99.6:
Changes in version 1.99.5:
clarification of docs/warning messages when “time” variable has too few timepoints to fit natural splines
bug fix in subset function: factor levels that don’t appear in subset pData are now dropped
Changes in version 1.99.4:
Changes in version 1.99.3:
Changes in version 1.99.2:
Changes in version 1.99.1:
Changes in version 0.99.0:
NEW FEATURES
Changes in version 1.3.4:
Changes in version 2.27:
NEW FEATURES
Changes in version 1.18.0:
NEW FEATURES
Changes in version 1.23.2:
BUG FIXES
Changes in version 1.23.1:
BUG FIXES
Changes in version 0.99.3:
getProfilesDataMultipleGenes: line 78: Test only Genetic Profiles having mRNA expression to get Profile Data.
getMutData(): line 96 change .GlobalEnv to myGlobalEnv)
getProfDataMultipleGenes(): line 7 add testCheckedCaseGenProf()
Changes in version 0.99.2:
Add documentation for RUN.GSEA() function
Remove dependency of RSvgDevice. This package is not available for Windows OS.
Changes in version 0.99.1:
Add examples in documents SIGNIFICANT USER-VISIBLE CHANGES
Add documentation for RUN.GSEA() function
Remove dependency of RSvgDevice. This package is not available for Windows OS.
Add examples in documents
Package released
Changes in version 0.99.6:
SIGNIFICANT USER-VISIBLE CHANGES
Bioconductor Release Candidate 7
Added CITATION file for citing Cardinal
BUG FIXES
Changes in version 0.99.5:
SIGNIFICANT USER-VISIBLE CHANGES
Bioconductor Release Candidate 6
Added new vignette for Cardinal design and development
Now using ProtGenerics generics for ‘spectra’, ‘peaks’, and ‘mz’
Changes in version 0.99.4:
SIGNIFICANT USER-VISIBLE CHANGES
Bioconductor Release Candidate 5
Updated vignette with biological examples
Added new citations to vignette
Changes in version 0.99.3:
SIGNIFICANT USER-VISIBLE CHANGES
Bioconductor Release Candidate 4
In plot and image methods, ‘groups’ arg now coerced to factor
BUG FIXES
Fixed bug in subset arg in select method
Fixed bug in plot and image methods with NA in ‘groups’ arg
Changes in version 0.99.2:
SIGNIFICANT USER-VISIBLE CHANGES
Bioconductor Release Candidate 3
Adjusts NIPALS unit tests for Windows build
Changes in version 0.99.1:
SIGNIFICANT USER-VISIBLE CHANGES
Bioconductor Release Candidate 2
Cleaned up biocViews
BUG FIXES
Changes in version 0.99.0 (2014-12-22):
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.6.0:
NEW FEATURES
Changes in version 2.20.0:
NEW FEATURES
Fingerprint search now provides E-values
New SDF plotting function, draw_sdf
Changes in version 1.9.2:
NEW FEATURES
Fusions data generated by tophat-fusion-post can be imported.
Star import function was improved.
Annotation of fusion is more robust as it it is clearly linked to specific genomic releases. e.g. h19 uses BSgenome.Hsapiens.UCSC.hg19 and TxDb.Hsapiens.UCSC.hg19.knownGene
Changes in version 3.0.1:
BUG FIXES
Changes in version 1.3.15:
Changes in version 1.3.14:
Changes in version 1.3.13:
update enrichPeakOverlap to support nShuffle = 0, which now will report only overlay with pvalue = NA <2015-03-29, Sun>
add facet and free_y parameter for plotAvgProf and plotAvgProf2 <2015-03-29, Sun>
update docs <2015-03-29, Sun>
update plotAvgProf and plotAvgProf2 to fully supporting confidence interval, see <2015-03-29, Sun>
Changes in version 1.3.12:
Changes in version 1.3.11:
Changes in version 1.3.10:
Changes in version 1.3.9:
Changes in version 1.3.8:
Changes in version 1.3.7:
Changes in version 1.3.6:
Changes in version 1.3.5:
Changes in version 1.3.4:
Changes in version 1.3.3:
Changes in version 1.3.2:
Changes in version 1.7.4:
Changes in version 1.7.3:
Changes in version 1.7.2:
Changes in version 1.7.1:
Changes in version 1.2.0:
More classification flexibility, now with parameter tuning integrated into the process.
New performance evaluation functions, such as a ROC curve and a performance plot.
Some existing predictor functions are able to return class scores, not just class labels.
Changes in version 1.5.4:
NEW FEATURES
BUG FIXES
Changes in version 1.5.3:
NEW FEATURES
BUG FIXES
Changes in version 1.5.2:
NEW FEATURES
BUG FIXES
Changes in version 1.5.1:
NEW FEATURES
Add buildClassifier function to save the classifier.
Add test file
predictTestSet also give a invisible output.
Add class “modelInfo”, “PASclassifier” and “featureVector”
BUG FIXES
Changes in version 1.5.3 (2015-02-02):
Changes in version 1.5.1 (2015-01-24):
Changes in version 1.3.2 (2015-04-04):
Changes in version 2.1.14:
Changes in version 2.1.13:
Changes in version 2.1.12:
user input is now supported with enricher and GSEA function <2015-04-01, Wed>
change use_internal_data parameter to … according to the change of DOSE <2015-04-01, Wed>
Changes in version 2.1.11:
Changes in version 2.1.10:
Changes in version 2.1.9:
throw stop msg when gene can not be mapped by DAVID <2015-03-12, Thu>
add return NULL when DAVID fail (no enrichment found or wrong ID type) <2015-03-11, Wed>
Changes in version 2.1.8:
Changes in version 2.1.7:
set includeAll = TRUE by default <2015-03-03, Tue>
added an includeAll option in plot(compareCluster) <2015-02-26, Thu> refer to:
fixed typo in groupGO <2015-02-26, Thu>
Changes in version 2.1.6:
Changes in version 2.1.5:
gseKEGG is also use online KEGG data by default. <2015-02-11, Wed>
change ‘use.KEGG.db’ parameter to ‘use_internal_data’, that can be used when I implement GO analysis with user specific annotation data <2015-02-11, Wed>
Changes in version 2.1.4:
update vignette <2015-02-11, Wed>
support formula like x ~ y + z, contributed by Giovanni Dall’Olio <2015-02-11, Wed>
add example of formula interface <2015-02-11, Wed>
formula interface for compareCluster contributed by Giovanni Dall’Olio <2015-02-11, Wed>
Changes in version 2.1.3:
update vignettes <2015-01-28, Wed>
fully support of using online version of KEGG in enrichKEGG, using online version is now by default of enrichKEGG <2015-01-28, Wed>
update CITATION <2015-01-28, Wed>
Changes in version 2.1.2:
support downloading latest KEGG annotation data <2015-01-27, Tue>
update vignette to use BiocStyle <2015-01-27, Tue>
Changes in version 2.1.1:
1.13.1: chromosome does not start from 1
Changes in version 0.99.3 (2015-04-02):
Changes in version 0.99.2 (2015-04-01):
Update indent based on the coding style of Bioconductor.
Trim long line.
Changes in version 0.99.1 (2015-03-31):
Add runnable examples for functions.
Update R version dependency from 2.10 to 3.2.
Add non-empty value sections for some functions.
Changes in version 0.99.0 (2015-03-27):
Changes in version 0.99.10 (2015-04-10):
Update regulationBiomart function and the pre-computed data associated because ENSEMBL has recently updated their schema in Biomart for these data.
Update the documentations (man and vignette)
Changes in version 0.99.9 (2015-03-10):
Update snpBiomart and structureBiomart functions and the pre-computed data associated because ENSEMBL has recently updated their schema in Biomart for these data.
Update the documentations (man and vignette)
Add the function compute.pvalue.cormatrix and allow the visualisation of only correlation under a significant level. (use the library psych)
Add the function comet.list to list the correlations between omic features
Replace capital letter by low letter
Update Shiny-based web application according to new functions
Changes in version 0.99.8 (2015-02-15):
Correction genesNameENSEMBL in order not to run if no ENSEMBL gene in the region of interest
Correction the error related to the loading of correlation matrice
Update the visualisation of Chromosome with the name of band (related to an update of Gviz)
Remove the visualisation of border for genes and transcripts to help the visualisation of different exons
Update the vignette about comet’s Shiny website and colors of tracks
Update the annotation tracks as Gviz was updated and now coMET can work on Gviz (version 1.10.9, current version)
Changes in version 0.99.7 (2014-12-19):
Changes in version 0.99.6 (2014-11-25):
add in “import IRanges and S4Vectors” in NAMESPACE
Fix mistakes in the vignette
Changes in version 0.99.5 (2014-11-06):
Changes in version 0.99.4 (2014-11-05):
Update the manual and the vignette
Fix little bugs
Update the annotation tracks using BiomartGeneRegionTrack of Gviz
Changes in version 0.99.3 (2014-10-25):
Update the manuel and the vignette
Update the function to create annotation tracks connecting to ENSEMBL mart (change of schema)
Fix little bug
Add the function to define the reference genome (cf the change of schema of ENSEMBL mart)
Changes in version 0.99.2 (2014-10-16):
Changes in version 0.99.1 (2014-10-16):
Add the package “BiocStyle” in Suggests of DESCRIPTION file
Change the absolute path to relative path of files (info file, expression file, and correlation file) in vignette and manual
Changes in version 0.99.0 (2014-09-24):
1.3.1: Added citation file
Changes in version 0.99.4:
cluster_rowsto FALSE but still cluster on rows.
Changes in version 0.99.2:
add two examples in vignette
add chunk labels in the vignette
Changes in version 0.99.1:
cell_funare now
unitobjects.
Changes in version 0.99.0:
Changes in version 1.99.4 (2015-04-08):
Changes in version 1.99.3 (2015-04-06):
Changes in version 1.99.2 (2015-03-21):
Provided vignette that allows R CMD CHECK –no-build-vignettes in <5 min
Fixed minor bug affecting runs in which not all samples are analyzed by CopywriteR function
Included a test for sorting of .bam files
Improved error messages
Fixed minor bug affecting plotting of samples
Fixed minor bug causing error when processing >100 samples simultaneously
Added support for capture regions bed files lacking the correct chromosome name prefix
Fixed minor bug affecting read count statistics on single-sample analysis
Changes in version 1.99.0 (2015-03-05):
Released new version
Improved the speed of the package
Implemented logging with the futile.logger package
Replaced direct slot or field access with the use of accessor functions
Implemented text wrapping
Replaced the use of bed-file format with GRanges objects
Created annotation and experiment packages
Addressed all NOTES upon R CMD CHECK
Restore options upon exit
Adjusted version numbering to 1.99.0
Implemented BiocParallel for parallel computing
Changed name from ENCODER to CopywriteR
Shortened lines to 80 characters
Added NEWS file
Changed F to FALSE
Changed T to TRUE
Added biocViews
Changed version to 0.99.0
Changes in version 0.99.0:
Changes in version 1.7.6:
NEW FEATURES
Changes in version 1.7.3:
NEW FEATURES
Changes in version 1.7.1:
BUG FIXES
Changes in version 1.1.28:
Added getWidths(), scaledAverage() and filterWindows(), to facilitate comparison of abundances during filtering.
Added findMaxima() to identify locally maximal windows from range data.
Added profileSites() to examine the coverage profile around specified regions, with wwhm() to guess the ideal window size from the profile.
Changed default window width in windowCounts() to 50 bp, default filter to a fixed count of 10. Also, filter=0 is honored when bin=TRUE.
Switched from the depracated rowData to rowRanges for all manipulations of SummarizedExperiment.
Changed all instances of
pet' to pe’ in read parameter
specification, and renamed getPETSizes() to getPESizes().
Removed the redundant rescue.pairs parameter in readParam().
Added fast.pe parameter in readParam(), for fast paired-end data extraction. Added dumpPE() to pre-process paired-end BAM files for fast downstream extraction.
Added support for custom column specification in getBestTest(), combineTests().
Switched from reporting average log-FC to numbers of up/down windows in combineTests().
Allowed getBestTest() to return all fields associated with the best window in the output table.
Added upweightSummits() to compute weights favouring high-abundance windows.
Added combineOverlaps(), getBestOverlaps() and summitOverlaps() wrapper functions for processing of Hits objects.
Added consolidateSizes(), to consolidate DB results from multiple window sizes.
Added support for custom key/name specification in detailRanges() for non-human/mouse systems.
Added support for strand-specific read extraction in readParam(), strand-specific counting via strandedCounts().
Added strand-awareness to mergeWindows(). Added protection against stranded input regions in extractReads(), detailRanges().
Changed algorithm for splitting of large peaks in mergeWindows().
Stored counting parameters in exptData for windowCounts(), regionCounts().
Fixed small inaccuracies with continuity correction addition in normalizeCounts() for NB-loess.
Switched to fragment midpoint for binning of paired-end data in windowCounts().
Added support for lists of library-specific readParam objects in windowCounts(), regionCounts(), correlateReads().
Added makeExtVector(), to support variable read extension lengths between libraries in windowCounts(), regionCounts().
Added support for read extension within extractReads().
Updated the user’s guide to reflect new and modified functions.
Added sra2bam.sh in inst/doc to reproducibly generate BAM files to run UG examples.
Cleaned up code in inst/tests for modified functions, added new tests for new functions.
2.9.3: Bugfix: - Introduced CHECK error by adding to .Rbuildignore…this is now fixed.
2.9.2: version bump to let BioC nightly build grab commit.
2.9.1: version bump for BioC devel release 3.1
2.8.2: Bugfixes: - removed reference to sqliteCloseConnection() (not exported by RSQLite 1.0.0) in vignette.
2.8.1: Bugfixes: - Made minimal changes for compatibility with RSQLite 1.0.0
Changes in version 1.5.1:
NEW FEATURES
BUG FIXES
Changes in version 1.15”)
1.01.01: 10-17-2014 Lorena Pantano lorena.pantano@gmail.com FIX BUG WHEN ONLY ONE GENE IS DEG
Changes in version 1.1.18:
BUG FIXES
Changes in version 1.1.17:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Polished the interaction with bumphunter >= 1.7.3
Updated the default cluster option now that BiocParallel::SnowParam() no longer has an ‘outfile’ argument.
Changes in version 1.1.16:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.1.15:
BUG FIXES
Changes in version 1.1.14:
BUG FIXES
maxRegionGapwas set to 300 instead of 0 in one step by default. Thus the process of mapping regions to genomic coordinates was messed up. If you have results prior to this fix you can try using to fix the results as much as possible. Basically, regions will be correct but the p-values will be approximated with the available information from the null regions. Truly fixing the p-values can only be done by re-running derfinder.
Changes in version 1.1.5:
NEW FEATURES
BUG FIXES
Changes in version 1.1.3:
NEW FEATURES
BUG FIXES
Changes in version 1.1.6:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.1.3:
BUG FIXES
Changes in version 1.8.0:
Changes in version 1.7.45:
Added a test in rlog for sparse data, mostly zero and some very large counts, which will give a warning and suggestion for alternate transformations.
Added plotSparsity() which will help diagnose issues for using rlog: data which do not resemble negative binomial due to many genes with mostly zeros and a few very large counts.
Changes in version 1.7.43:
Changes in version 1.7.32:
Changes in version 1.7.11:
Changes in version 1.7.9:
Added Genome Biology citation for the DESeq2 methods.
Introduced type=”iterate” for estimateSizeFactors, an alternative estimator for the size factors, which can be used even when all genes have a sample with a count of zero. See man page for details.
Changes in version 1.7.3:
Changes in version 1.13.5:
Changes in version 1.13.4:
Roll up all updates
Update DESeq2 reference in vignette; fix vignette samplesheet
use vennPlot from systemPiper
Changes in version 1.13.3:
Fix Makevars to avoid gnu-specific extensions
Replace ‘require’ with ‘requireNamespace’ to eliminate NOTEs regarding misuse of ‘require’
Remove non-ASCII characters from a couple of comments
Changes in version 1.13.2:
Changes in version 1.13.1:
New: color vector lists for dba.plotHeatmap and colos for dba.plotPCA labels
Fix: bug causing two plots when changing score in dba.plotHeatmap and dba.plotPCA
Changes in version 0.99.0:
Changes in version 2.5.12:
report NA in qvalue column when it fail to calculate instead of throw error <2015-03-09, Thu>
update IC data <2015-03-08, Wed>
Changes in version 2.5.11:
Changes in version 2.5.10:
implement enrichNCG and now gseAnalyzer accept setType = “NCG” <2015-04-01, Wed> see
change use_internal_data parameter to … in all S3 generics and methods <2015-04-01, Wed>
Changes in version 2.5.9:
Changes in version 2.5.8:
Changes in version 2.5.7:
Changes in version 2.5.6:
Changes in version 2.5.5:
Changes in version 2.5.3:
Changes in version 2.5.1:
Changes in version 2.5.0:
Changes in version 2.3.4:
Bioc. API changes: added missing imports, removed unneeded imports, added a missing package dependency
Removed generics now defined in BiocGenerics
Changes in version 2.3.3:
Changes in version 2.3.2:
Changes in version 2.3.1:
Changes in version 2.3.0:
Changes in version 4.10.0:
NEW FEATURES
‘paintObjects’ allows control over behavior at image edges
‘getFrames’ function returning a list of Image objects
default ‘display’ method can be set by options(“EBImage.display”)
‘short’ argument to the Image ‘print’ method
‘equalize’ function performing histogram equalization
SIGNIFICANT USER-VISIBLE CHANGES
‘translate’ moves the image in the opposite direction as before
‘rotate’ returns an image centered in a recalculated bounding box
‘as.Image’ coerces subclasses to Image objects
‘getFrame’ returns individual channels of a Color image as Grayscale frames
‘display’ method defaults to ‘raster’ unless used interactively
‘combine’ allows to combine images of the same color mode only
PERFORMANCE IMPROVEMENTS
‘filter2’: calculate FFT using methods from the ‘fftwtools’ package
‘as.nativeRaster’: now implemented in C
‘medianFilter’: double to integer conversion moved to C code
‘hist’: fixed binning issues and improved performance
BUG FIXES
‘medianFilter’: fixed multi-channel image handling; preserve original object class
‘as.nativeRaster’: allow for an arbitrary number of color channels
‘display’: set missing color channels to blank
Changes in version 1.7.1:
In EBSeq 1.7.1, EBSeq incorporates a new function GetDEResults() which may be used to obtain a list of transcripts under a target FDR in a two-condition experiment. The results obtained by applying this function with its default setting will be more robust to transcripts with low variance and potential outliers. By using the default settings in this function, the number of genes identified in any given analysis may differ slightly from the previous version (1.7.0 or order). To obtain results that are comparable to results from earlier versions of EBSeq (1.7.0 or older), a user may set Method=”classic” in GetDEResults() function, or use the original GetPPMat() function. The GeneDEResults() function also allows a user to modify thresholds to target genes/isoforms with a pre-specified posterior fold change.
Also, in EBSeq 1.7.1, the default settings in EBTest() and EBMultiTest() function will only remove transcripts with all 0’s (instead of removing transcripts with 75th quantile less than 10 in version 1.3.3-1.7.0). To obtain a list of transcripts comparable to the results generated by EBSeq version 1.3.3-1.7.0, a user may change Qtrm = 0.75 and QtrmCut = 10 when applying EBTest() or EBMultiTest() function.
Changes in version 2.1:
Fixed bug in plotPCA: parameter k was not passed properly in SeqExpressionSet method.
Fixed bug in plotQuality: trimming when reads of different lengths in same BAM/FASTQ files.
Changes in version 3.10.0:
An DGEList method for romer() has been added, allowing access to rotation gene set enrichment analysis.
New function dropEmptyLevels() to remove unused levels from a factor.
New argument p.value for topTags(), allowing users to apply a p-value or FDR cutoff for the results.
New argument prior.count for aveLogCPM().
New argument pch for the plotMDS method for DGEList objects. Old argument col is now removed, but can be passed using …. Various other improvements to the plotMDS method for DGEList objects, better labelling of the axes and protection against degenerate dimensions.
treatDGE() is renamed as glmTreat(). It can now optionally work with either likelihood ratio tests or with quasi-likelihood F-tests.
glmQLFit() is now an S3 generic function.
glmQLFit() now breaks the output component s2.fit into three separate components: df.prior, var.post and var.prior.
estimateDisp() now protects against fitted values of zeros, giving a more accurate estimate of prior.df.
DGEList() now gives a message rather than an error when the count matrix has non-unique column names.
Minor corrections to User’s Guide.
requireNamespace() is now used internally instead of require() to access functions in suggested packages.
Changes in version 1.1.1:
NEW FEATURES
de.ana: now based on limma functionality
ggea.graph: extended control of layout
ggea: * permutation p-value now based on fast edge resampling * p-value approximation now based on gaussian mixture * extended control for edge selection (consistency threshold, edge type, …)
Changes in version 0.99.17:
NEW FEATURES
Changes in version 0.99.16:
SIGNIFICANT USER-VISIBLE CHANGES
Added argument outfile to ensDbFromGtf that allows to manually specify the file name of the database file.
ensDbFromGtf tries now to automatically fetch the sequence lengths from Ensembl.
BUG FIXES
Changes in version 0.99.15:
NEW FEATURES
metadata method to extract the information from the metadata database table.
ensDbFromGtf function to generate a EnsDb SQLite file from an (Ensembl) GTF file.
Changes in version 0.99.14:
BUG FIXES
Changes in version 0.99.13:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.12:
BUG FIXES
Changes in version 1.8.0:
NEW FEATURES
Add VEPParam78 class to support Ensembl 78
Add ‘flag_pick’, ‘flag_pick_allele’, ‘pick_order’ and ‘tsl’ flags
MODIFICATIONS
Changes in version 1.1.1:
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES AND MINOR IMPROVEMENTS
Changes in version 3.2:
NEW FEATURES
HTML vignette
Bipartite network: Nodes are now circles and squares (only available for “static” plot)
PlotGoAncestors: added argument nCharTerm
clustersDistance: added argument ‘clustMethod’ and set “average” as default clustering method.
GO evidence: Added argument to fea_topGO (new data object available: GOEvidenceCodes)
Added argument vExprColors to functionalNetwork.
Vertex size now allows to set a value for each gene.
BUGFIXES
Changes in version 0.99:
Multi probe support
Improved speed
Parameters are now stored in arguments.txt file
Changes in version 1.5.15:
correct a bad memory managment in readgroup.cpp (do not use erase on a vector!)
correct a bug that may happen when the pre-processing encountered a * in the CIGAR field. now it simply ignore the read (align.cpp).
Changes in version 1.5.14:
correct a bug which might happened when reading the RG:Z tag in the SAM file (align.cpp)
allow H characters in the CIGAR field
correction in spams (prox/project.h) related to topological order
Changes in version 1.5.12:
MAJOR CHANGES
NEW FEATURES
Changes in version 1.5.11:
Changes in version 1.5.10:
MAJOR CHANGES
NEW FEATURES
MINOR CHANGES
change a bit the paired-end graph paradigm. Ensure that one isoform is one unique path in the graph, as for single-end graph.
[parameter] add the delta (poisson offset in the loss) parameter as an option, in case of fine-tuning.
[parameter] the cutoff option is now active for both single and paired, and the default value is 1%.
Changes in version 1.5.8:
Changes in version 1.5.7:
Changes in version 1.5.6:
MAJOR CHANGES
faster single-end and paired-end graph implementation
use_TSSPAS: if yes then start/end bins are the ones with no entering/outgoing junctions (+ annotated ones if given annotations)
MINOR CHANGES
remove the sanity-check for possibly duplicated types, as it was solved into readgroup.cpp/getType
[pre-processing] back to default 1 for minJuncCount (I changed my mind !!)
[pre-processing] cancel change of version 1.3.9 (extreme boundary of segments calculateBound in readgroup.cpp) (I changed my mind !!)
Changes in version 1.5.5:
allow more easy 2 steps run (preprocessing+prediction). The option “OnlyPreprocess” allows to perform preprocessing only. It creates two files ‘prefix.instance’ and ‘prefix.totalnumread’. Running then flipflop with the option preprocess.instance=’prefix.instance’ performs the prediction (it reads automatically the total number of reads in prefix.totalnumread)
[pre-processing] push the default minJuncCount from 1 to 2 (high enough for a default?)
[pre-processing] slight change for paired-end preprocessing, see option to processsam (–single-only not automatic anymore)
start using Rprintf in c/cpp codes for user messages (to continue)
Changes in version 1.5.4:
Changes in version 1.5.3:
NEW FEATURE
Changes in version 1.5.1:
Changes in version 1.2.0:
NEW FEATURES
addTrajectory: changed implementation in the addTrajectory function, notable gain in computing time
particles: implementation of particles() now used BiocParallel - massive gain in performances!
snap() function to allow interaction of the user with the image, to display additional information on the trajectories identified on the Frames/ParticleSet
shinyFlow() released! A Shiny App is delivered along with the package, documentation is available to guide exploration of data and parameters
Jupyter/IPython notebooks available in the installed folder of the package - provided as template for further analysis
Vignette: updated to reflect the current implementation and newest features
preprocess.Frames: extended documentation
BiocViews: added a couple of terms that fit better with current status of the package
Added url for development version on github. Active development is performed there, therefore feel free to send pull requests/ feature wishes ()!
Added integration of the repository with Travis-CI
add.contours: if image is in grayscale, use false colours to enhance detected particles
plot2d.TrajectorySet is now able to draw a grid and help backtracking points from the trajectories
BUG FIXES
select.Frames: fixed behaviour in select.Frames when selecting a single frame
add.contours: corrected bug in add.contours for grayscale images, was preventing correct combining of images. now uses correctly false colours and aids identification
particles: for computing particles,added check whether dimnames is set or not. previously it raised an error, but it was kind of overkilling
fixed behaviour in export.Frames
typos fixed
Vignette: fixed typos, fixed parameter names in the preprocessing steps
read.Frames: additional check on the existence of all files
Grayscale images can now be directly preprocessed by selecting channel = “all”
Changes in version 1.5.1:
USER VISIBLE CHANGES
Remove functions that support computation of permutation-based p-values of the Friedman- Rafsky (FR) statistic,including permutePops() and getFRvalsPerm(). Current release computes p-values of the FR statistic directly from the standard normal curve.
Remove functions for building a reference sample for multiple flow cytometry sample comparisons, including makeRefMap() and makeRefSample(). Instead, curent release encourages the user to generate a multi-sample similar matrix of cell populations which can in turn be used to decide on matched or mismatched cell populations
Remove getSomePops(), which was used to compute selected cell population pairs in a cross-sample comparison. Current release computes the FR statistics for all possible cell population pairs in a cross-sample comparison.
Changes in version 0.99.2:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.0:
SIGNIFICANT USER-VISIBLE CHANGES
Included addition unit tests.
Version first submitted to BioConductor.
Changes in version 0.99.4:
NEW FEATURES
Changes in version 0.99.0:
NEW FEATURES
Changes in version 2.7.0:
Changes in version 1.19:
Correct citation for use of frma with Gene and Exon ST arrays added.
The internal workings of the frma function have been modified to ease the eventual transition AffyBatch (affy) objects to FeatureSet (oligo) objects as input.
Changed the way in which the user can pass their own fRMA vectors to the frma function via the “input.vecs” argument. Previously, the user could supply a partial set of vectors and the remaining ones would be obtained from the default frmavecs packages. In retrospect, this seems very likely to introduce a mistake. Now, the user has to either supply all of their own vectors or use all of the default vectors. If anyone was mixing vectors before, this can still be accomplished by loading the respective frmavecs package and manually creating your own mixture of vectors.
Bug fix: on certain operating systems, due to differences in the locale, the probe ordering returned by the pm function (affy) did not match the order stored in the frmavecs packages. Updated frmavecs packages will now contain the pmindex values for all probes and affy ids for all probesets. Also the frma and barcode functions now check that the order matches. If the order is not the same, these functions attempt to reorder the probes to match.
Added NEWS.Rd file.
Changes in version 1.11.3:
BUGFIX: The wiki2cmap function now excludes empty files downloaded from wikipathways from parsing.
BUGFIX: The go2cmap function is now exported.
BUGFIX: The reactom2cmap function is currently defunct, because the reactome.db package is broken.
Changes in version 1.11.2:
Changes in version 1.11.1:
Changes in version 1.11.0:
Changes in version 1.7.2:
Changes in version 1.7.1:
Changes in version 1.3.0-1.3.10:
NEW FEATURES
a new argument ‘visible’ is added to the functions
add.gdsn(),
addfile.gdsn() and
addfolder.gdsn()
objdesp.gdsn() returns ‘encoder’ to indicate the compression
algorithm
add a new function
system.gds() showing system configuration
support efficient random access of zlib compressed data, which are composed of independent compressed blocks
support LZ4 compression format (), based on “lz4frame API” of r128
allow R RAW data (interpreted as 8-bit signed integer) to replace
32-bit integer with
read.gdsn(),
readex.gdsn(),
apply.gdsn(),
clusterApply.gdsn(),
write.gdsn(),
append.gdsn()
a new argument ‘target.node’ is added to
apply.gdsn(), which allows
appending data to a target GDS variable
apply.gdsn(),
clusterApply.gdsn(): the argument ‘as.is’ allows
“logical” and “raw”
more argument checking in
write.gdsn()
new components ‘trait’ and ‘param’ in the return value of
objdesp.gdsn()
add new data types: packedreal8, packedreal16, packedreal32
a new argument ‘permute’ in the function
setdim.gdsn()
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
minor fixes
v1.3.2: fixes
v1.3.3: minor fixes, ‘sync.gds’ synchronizes the GDS file
v1.3.4: fixes
v1.3.5: fixes
Changes in version 1.9.1:
NEW FEATURES
BUG FIXES
Changes in version 0.99.4:
Changes in version 0.99.0:
Changes in version 1.6.1:
Vignette update
Added Spearman and Kendall correlations (argument correlationMethod)
Changes in version 0.99.9:
IMPROVEMENTS AND BUG FIXES
Changes in version 0.99.8:
IMPROVEMENTS AND BUG FIXES
added the Bioinformatics citation
vignette is converted to html format
changed tests form test_that to RUnit
Changes in version 0.99.0.2:
IMPROVEMENTS AND BUG FIXES
Changes in version 0.99.0.1:
NEW FUNCTIONS AND FEATURES
IMPROVEMENTS AND BUG FIXES
Changes in version 0.99:
NEW FUNCTIONS AND FEATURES
new plotting functions for visualization of ScoreMatrix and ScoreMatrixList multiHeatMatrix, heatMatrix, metaHeat and metaPlot
ScoreMatrix constructor can deal with a variety of inputs, including BAM and wig
Changes in version 1.23.2:
Changes in version 1.23.1:
Changes in version 1.23.0:
Changes in version 1.22.3:
Changes in version 1.22.2:
Changes in version 1.22.1:
Changes in version 1.4.0:
NEW FEATURES
SIGNIFICANT USER-LEVEL CHANGES
Add mapToAlignments(), pmapToAlignments(), mapFromAlignments(), and pmapFromAlignments() as replacements for the “mapCoords” and “pmapCoords” methods for GAlignments objects.
Clarify use of ‘fragments’ in summarizeOverlaps() man page.
Tweak “show” method for GAlignments objects to display a shorter version of long CIGARs.
Add checks and more helpful error message for summarizeOverlaps() when “file does not exist”
DEPRECATED AND DEFUNCT
Deprecated readGAlignment*FromBam() functions in favor of readGAlignments(), readGAlignmentPairs(), readGAlignmentsList() and readGappedReads().
Deprecated “mapCoords” and “pmapCoords” methods.
Removed Lngap(), Rngap(), introns(), and makeGAlignmentsListFromFeatureFragments() functions, and “ngap”, “map”, “pmap”, and “splitAsListReturnedClass” methods (were defunct in GenomicAlignments 1.2.0).
BUG FIXES
Changes in version 1.20:
NEW FEATURES
Add makeTxDbFromGRanges() for extracting gene, transcript, exon, and CDS information from a GRanges object structured as GFF3 or GTF, and returning that information as a TxDb object.
TxDb objects have a new column (“tx_type” in the “transcripts” table) that the user can request thru the ‘columns’ arg of the transcripts() extractor. This column is populated when the user makes a TxDb object from Ensembl (using makeTxDbFromBiomart()) or from a GFF3/GTF file (using makeTxDbFromGFF()), but not yet (i.e. it’s set to NA) when s/he makes it from a UCSC track (using makeTxDbFromUCSC()). However it seems that UCSC is also providing that information for some tracks so we’re planning to have makeTxDbFromUCSC() get it from these tracks in the near future. Also low-level makeTxDb() now imports the “tx_type” column if supplied.
Add transcriptLengths() for extracting the transcript lengths from a TxDb object. It also returns the CDS and UTR lengths for each transcript if the user requests them.
extractTranscriptSeqs() now works on a FaFile or GmapGenome object (or, more generally, on any object that supports seqinfo() and getSeq()).
SIGNIFICANT USER-VISIBLE CHANGES
Renamed makeTranscriptDbFromUCSC(), makeTranscriptDbFromBiomart(), makeTranscriptDbFromGFF(), and makeTranscriptDb() -> makeTxDbFromUCSC(), makeTxDbFromBiomart(), makeTxDbFromGFF(), and makeTxDb(). Old names still work but are deprecated.
Many changes and improvements to makeTxDbFromGFF(): - Re-implemented it on top of makeTxDbFromGRanges(). - The geneID tag, if present, is now used to assign an external gene id to transcripts that couldn’t otherwise be linked to a gene. This is for compatibility with some GFF3 files from FlyBase (see for example dmel-1000-r5.11.filtered.gff included in this package). - Arguments ‘exonRankAttributeName’, ‘gffGeneIdAttributeName’, ‘useGenesAsTranscripts’, and ‘gffTxName’, are not needed anymore so they are now ignored and deprecated. - Deprecated ‘species’ arg in favor of new ‘organism’ arg.
Some tweaks to makeTxDbFromBiomart(): - Drop transcripts with UTR anomalies with a warning instead of failing. We’ve started to see these hopeless transcripts with the release 79 of Ensembl in the dmelanogaster_gene_ensembl dataset (based on FlyBase r6.02 / FB2014_05). With this change, the user can still make a TxDb for dmelanogaster_gene_ensembl but some transcripts will be dropped with a warning. - BioMart data anomaly warnings and errors now show the first 3 problematic transcripts instead of 6.
‘gene_id’ metadata column returned by genes() is now a character vector instead of a CharacterList object.
DEPRECATED AND DEFUNCT
Deprecated makeTranscriptDbFromUCSC(), makeTranscriptDbFromBiomart(), makeTranscriptDbFromGFF(), and makeTranscriptDb(), in favor of makeTxDbFromUCSC(), makeTxDbFromBiomart(), and makeTxDbFromGFF(), and makeTxDb().
Deprecated species() accessor in favor of organism() on TxDb objects.
sortExonsByRank() is now defunct (was deprecated in GenomicFeatures 1.18)
Removed extractTranscriptsFromGenome(), extractTranscripts(), determineDefaultSeqnameStyle() (were defunct in GenomicFeatures 1.18).
BUG FIXES
makeTxDbFromBiomart(): - Fix issue causing the download of ‘chrominfo’ data frame to fail when querying the primary Ensembl mart (with host=”ensembl.org” and biomart=”ENSEMBL_MART_ENSEMBL”). - Fix issue with error reporting code: when some transcripts failed to pass the sanity checks, the error message was displaying the wrong transcripts. More precisely, many good transcripts were mistakenly added to the set of bad transcripts and included in the error message.
extractTranscriptSeqs(): fix error message when internal call to exonsBy() fails on ‘transcripts’.
Changes in version 1.4.0:
NEW FEATURES
Add reduceFiles() and reduceRanges()
Add ‘algorithm’ argument to summarizeOverlaps methods
Add REDUCEsampler() from Martin
MODIFICATIONS
Deprecate *FileViews classes
Modify show() for GenomicFiles class
Add ‘Chunking’ section to vignette
Update vignette figures
Change REDUCE default from
+ to
c for reduceByYield()
BUG FIXES
Changes in version 1.20.0:
NEW FEATURES
Add coercion methods to go back and forth between ExpressionSet and SummarizedExperiment.
Add ‘assayNames’, ‘assayNames<-‘ for SummarizedExperiment
assays() supports arrays of up to 4 dimensions.
Add GNCList() for preprocessing a GenomicRanges object into a GNCList object that can be used for fast overlap seach with findOverlaps(). GNCList() is a replacement for GIntervalTree() that uses Nested Containment Lists instead of interval trees. Unlike GIntervalTree(), GNCList() supports preprocessing of a GenomicRanges object with ranges located on a circular sequence.).
All “findOverlaps” methods now support ‘select’ equal “last” or “arbitrary” (in addition to “all” and “first”).
Add absoluteRanges() and relativeRanges() to transform back and forth between absolute and relative genomic ranges.
SIGNIFICANT USER-LEVEL CHANGES
Renamed ‘rowData’ and ‘rowData<-‘ -> ‘rowRanges’, ‘rowRanges<-‘. Old names still work but are deprecated.
Some improvements to makeGRangesFromDataFrame(): - Improve internal logic used for finding the GRanges columns in the input. - If ‘seqinfo’ is not supplied, the seqlevels are now ordered according to the output of GenomeInfoDb::rankSeqlevels(). - Now an attempt is made to turn ‘df’ into a data frame (with ‘as.data.frame(df)’) if it’s not a data frame or a DataFrame object.
The GRanges() constructor now propagates the metadata cols that are on ‘ranges’ if no metadata cols are explicitly passed to the constructor.
DEPRECATED AND DEFUNCT
Deprecated ‘rowData’ and ‘rowData<-‘ in favor of ‘rowRanges’ and ‘rowRanges<-‘. GIntervalTree objects.
Removed “map” and “splitAsListReturnedClass” methods (were defunct in GenomicRanges 1.18.0).
Removed makeSeqnameIds() (was defunct in GenomicRanges 1.18.0).
Removed ‘with.mapping’ argunment from “reduce” methods (was defunct in GenomicRanges 1.18.0).
BUG FIXES
Fix ‘findOverlaps(…, type=”start”)’ on GRangesList objects which has been broken for years.
Fix self overlap search on a GRanges object when ‘ignore.strand=TRUE’ (i.e. ‘findOverlaps(gr, ignore.strand=TRUE)’).
Changes in version 1.1.14:
Changes in version 1.21.10:
NEW FEATURES
Changes in version 5.3:
new VCF extract for demonstrating cisAssoc VCF-SummarizedExperiment analysis
GGtools kept for legacy/migration purposes only; use gQTLBase and gQTLstats instead
Changes in version 0.99.28:
Changes in version 0.99.27:
Changes in version 0.99.26:
update geom_tiplab <2015-03-31, Tue>
update plot method of beast <2015-03-17, Tue>
Changes in version 0.99.25:
Changes in version 0.99.24:
use “round” segment end, look very better <2015-03-12, Thu>
update vignett <2015-03-11, Wed>
Changes in version 0.99.23:
mv geom_hilight to hilight <2015-03-11, Wed>
mv geom_phylopic to phylopic <2015-03-11, Wed>
implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
Changes in version 0.99.22:
Changes in version 0.99.21:
Changes in version 0.99.19:
Changes in version 0.99.18:
Changes in version 0.99.17:
Changes in version 0.99.16:
Changes in version 0.99.15:
Changes in version 0.99.14:
Changes in version 0.99.13:
Changes in version 0.99.12:
update vignette <2015-02-04, Wed>
gzoom methods that supports all tree objects <2015-02-04, Wed>
geom_hilight layer for highlighting clade <2015-02-04, Wed>
Changes in version 0.99.11:
add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>
revised groupOTU that output index can be used in geom_text and update vignette <2015-02-04, Wed>
Changes in version 0.99.10:
support y scale by category variable <2015-02-03, Tue>
support order nodes by yscale <2015-02-03, Tue>
Changes in version 0.99.9:
Changes in version 0.99.8:
Changes in version 0.99.7:
Changes in version 0.99.6:
read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon>
now read.beast supports characters in support values <2015-01-18, Sun>
add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
implement groupOTU methods <2015-01-14, Wed>
export get.offspring.tip <2015-01-14, Wed>
Changes in version 0.99.5:
move ape and ggplot2 from Depends to Imports <2015-01-12, Mon>
get.tipseq method for paml_rst and codeml object <2015-01-08, Thu>
add gzoom function, similar to zoom function in ape <2015-01-07, Wed>
add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
remove «- and update vignette <2015-01-06, Tue>
update vignette and use BibTex and CSL for references <2015-01-05, Mon>
update cladogram layout <2015-01-05, Mon>
read.baseml function and update vignette with baseml example <2015-01-04, Sun>
plot method for hyphy and hyphy example in vignette <2015-01-04, Sun>
merge all vignettes to ggtree vignette <2015-01-04, Sun>
Changes in version 0.99.4:
ggtree now support branch.length = “none” to only draw tree topology <2015-01-03, Sat>
get.subs method for hyphy object <2015-01-03, Sat>
show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
export read.hyphy <2015-01-02, Fri>
export hyphy class <2015-01-01, Thu>
plot method for beast class and get.tree method for codeml class <2014-12-31, Wed>
show, get.fields, get.subs and plot methods for codeml class <2014-12-30, Tue>
plot method for paml_rst class <2014-12-30, Tue>
get.subs, method for paml_rst class <2014-12-30, Tue>
show, plot, get.tree and fority methods for codeml_mlc class <2014-12-29, Mon>
codeml class <2014-12-29, Mon>
hyphy class and read.hyphy prototype <2014-12-27, Sat>
update man file and add example file of beast output <2014-12-26, Fri>
get.tree and get.fileds methods of beast class <2014-12-26, Fri>
read.beast <2014-12-26, Fri>
beast class and show method <2014-12-26, Fri>
coplot prototype<2014-12-24, Wed>
parse translation matrix in beast nexus <2014-12-24, Wed>
extract beast stats info <2014-12-23, Tue>
Changes in version 0.99.3:
gplot function that can view a tree and an associated matrix simultaneously <2014-12-22, Mon>
modified vignette to show based on branch position and break the evolution distance scale <2014-12-22, Mon>
label and annotation can be put based on branch. <2014-12-22, Mon>
write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun>
support unrooted layout in ggplot. <2014-12-21, Sun>
support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun>
Changes in version 0.99.2:
layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34 of ‘Inferring Phylogenies’ (page 578-580) <2014-12-20, Sat>
add layout parameter in ggtree and geom_tree, now supports phylogram and cladogram <2014-12-20, Sat>
%<+% function for inserting annotation data to a tree view <2014-12-20, Sat>
update ggtree-treeAnnotation vignette <2014-12-20, Sat>
Changes in version 0.99.1:
%<% function for updating tree view with a new tree <2014-12-19, Fri>
add examples in man files <2014-12-19, Fri>
Changes in version 1.1.12:
NEW FEATURES
Changes in version 1.1.11:
NEW FEATURES
Changes in version 1.1.10:
BUG FIX
Changes in version 1.1.9:
TYPOS
Changes in version 1.1.8:
TYPOS
Changes in version 1.1.7:
BUG FIXES
Changes in version 1.1.6:
BUG FIXES
NEW FEATURES
New function pValue_GO() allows calculation of P-value for each ontology using permutation of genes labels. This allows users to estimate the chance of seeing a GO term reach a particular rank (or score). Features a fancy progres bar shamelessly adapted from StackOverflow.
heatmap_GO now semi-autmoatically resizes the bottom and right margins to accomodate large gene and sample labels, respectively. The user may control those margins using the “margins” argument of the function.
heatmap_GO default call now shows the gene feature identifier for those missing an annotated gene name, when gene names are requested (also the default).
A rank.by slot is now created by the GO_analyse() function in the result object to state the metric used to order the result tables.
a filters.GO slot stating the filters and cutoffs applied to the result object is now created or updated by successive uses of the subset_scores() function. Warnings and notes are displayed if conflicting filters and cutoffs are applied on a previously filtered result object.
rerank() function now supports re-ordering by P-value. Note that this is only applicable to the output of the pValue_GO() function mentioned above.
rerank() function now updates the rank.by slot of the result object to state the current ordering metric.
subset_scores() function now allows filtering by P-value. Note that this is only applicable to the output of the pValue_GO() function mentioned above.
Backward compatibility with Ensembl annotation releases 75 and earlier, which used ‘external_gene_id’, which was renamed to ‘external_gene_name’ in releases 76 and later.
table_genes() function defaults to sorting genes by decreasing score (equivalent to increasing rank). Gene feature name or identifier are supported alternative filters for sorting.
UPDATED FEATURES
Allow user to override row_labels in heatmap_GO. This way, the color-coding of the sample can be kept, while better description of the samples can be used to label them, instead of the phenodata values.
In heatmap_GO(), if the labRow argument is of length 1, it is assumed to be the name of a column in the phenoData slot. Useful to re-label subsetted ExpressionSet objects.
GENERAL UPDATES
Updated the AlvMac training dataset to include ‘RPL36A’ an example of multiple Ensembl gene identifier annotated to the same gene name.
Updated the AlvMac example custom annotations to match the updated dataset.
Updated the example AlvMac_results to match the updated dataset.
Set the random seed prior to running the GO_analyse() example in the vignette. Hopefully, this should allow reproducible testing by the users.
In User Guide, load package before loading the attached data.
In User Guide, new sections and examples dealing with the re-labelling of heatmap samples, the use of P-values, the re-ranking and subsetting of results using P-values. New sub-sections for clarity. Emphasis on the use and generation of local annotation, rather than use of current online Ensembl annotation release.
No more code connecting to the Ensembl server in any the help files and User Guide.
Help pages examples with more consistent indentation of code.
Changes in version 1.1.5:
BUG FIXES
Changes in version 1.1.4:
NEW FEATURES
Custom annotations can be provided to the GO_analyse function using three new arguments: “GO_genes”, “all_GO”, and “all_genes”. See below for individual description.
The GO_genes argument allows the user to provide associations between feature identifiers in the ExpressionSet and gene ontology identifiers. This will skip all calls to the Ensembl BioMart server. Consequently, we recommend the use of the “all_GO” and “all_genes” arguments whenever “GO_genes” is used. Otherwise, some downstream functions may not work. For instance, the expression_plot, expression_profiles, and heatmap_GO function can be used to generate plots,although lacking gene and gene ontology names. See below for more details.
The all_GO argument allows the user to provide the name and namespace (“biological_process”, “molecular_function”, or “cellular_component”) corresponding to gene ontology identifiers. This enables subsequent filtering of result tables by namespace, and annotation of heatmaps with the name of the gene ontology.
The all_genes argument allows the user to provide the name and description corresponding to feature identifiers in the ExpressionSet. This enables annotation of expression plots with the gene name associated with the feature.
UPDATED FEATURES
In the GO_analyse function, the eSet argument is now formally checked to be of class ExpressionSet prior to any calculation. If not, the function returns an appropriate error message.
The error messages caused when the user gives a name that does not exist in the phenoData slot of the ExpressionSet were updated to use the word “column”, rather than “factor”.
GENERAL UPDATES
Updated the help page for function GO_analyse to describe the new features described above and provide a code example.
Used the BiocStyle package to format the vignette.
Added a new section in the vignette to document the new features described above.
Added a new section in the vignette to mention the creation of shiny applications using the output of GOexpress. Included a screenshot of a shiny application developed from the original AlvMac dataset.
Added a new section in the vignette to highlight the availability of a “subset” argument to avoid the need for additional ExpressionSet objects to analyse or visualise subsets of samples.
Changes in version 1.1.3:
NEW FEATURES
Included private function used to generate the prefix2dataset table.
Included private function used to generate the microarray2dataset table.
GO_analyse states the number of gene features in the given dataset that were found in the BioMart dataset. This allows the user to interrupt the script if a suspiciously low number of mapped features suggests an incorrect BioMart dataset was used.
UPDATED FEATURES
Updated the prefix2dataset table. Three more species (“Chlorocebus sabaeus”, “Papio anubis” , and “Poecilia formosa”), and two more columns (“species” and “sample”).
Updated the microarray2dataset table. Probeset patterns are now hard coded in the package, but dynamically defined as unique to a platform (or not) by the function building the microarray2dataset table. Species without microarray platforms were also included in the table with NA values. Code was added in the GO_analyse method to ignore those before trying to resolve the origin of the expression data, if not specified by the user.
Renamed column “prefix” to “pattern” in microarray2dataset table.
Disabled manual check of C. elegans and D. melanogaster, as the automated detection is doing the exact same thing. Only S. cerevisiae requires a manual check of the “Y” prefix instead of the automatically extracted “Y[:LETTERS:]{2}” pattern.
Methods expression_plot_symbol and expression_profiles_symbol now return the list of gene feature identifiers instead of NULL when multiple plots are produced. That may be confusing as they return the list of close matches when an invalid gene symbol was given, and they return the ggplot when obly one plot is produced.
GENERAL UPDATES
Changes in version 1.1.2:
GENERAL UPDATES
Changes in version 1.1.1:
BUG FIXES
Ensembl BioMart has changed the column ‘external_gene_id’ to ‘external_gene_name’. Renamed my biomaRt queries accordingly to prevent GO_analyse() from crashing during the analysis step.
Updated the AlvMac_results variable containing sample results annotated with the deprecated ‘external_gene_id’. It now includes the new ‘external_gene_name’.
GENERAL UPDATES
DESCRIPTION file minor correction.
User Guide’s chunk about installation using biocLite is not evaluated anymore, as advised by Dan Tenenbaum.
Changes in version 1.0.0:
NEW FEATURES
Authentication support for native apps, service accounts, and API keys.
Support for retreiving Reads and Variants.
Simple converters to GAlignments for Reads, and GRanges and VRanges for Variants.
Changes in version 1.25.5:
Changes in version 1.25.4:
Changes in version 1.25.3:
add doi in CITATION <2015-01-28, Wed>
update vignette using BiocStyle <2015-01-26, Mon>
Changes in version 1.25.2:
Changes in version 1.25.1:
Changes in version 1.13.2 (2015-04-02):
Pathways for multiple species: see pathwayDatabases() output.
Native pathway IDs.
Removed SPIKE database.
Deprecated objects: biocarta, humancyc, kegg, nci, panther, reactome.
Deprecated functions: runClipperMulti, runDEGraphMulti, runTopologyGSAMulti.
Changes in version 0.99.3:
Changes in version 0.99.2:
gtrellis_infoto
gtrellis_show_index
Changes in version 1.11.0:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
Streaming behaviour for BiomartGeneRegionTracks. Already queried regions are cached, and new data is fetched from Biomart on demand.
Proper handling of UCSC genome identifiers in BiomartGeneRegionTracks. Automated mapping to Ensembl genome versions and Biomart archives.
BUG FIXES
Changes in version 1.13.27:
Changes in version 1.13.26:
Changes in version 1.13.24:
Changes in version 1.13.23:
Changes in version 1.13.22:
Removed “outfile” arguments from batchChisqTest, batchFisherTest, and mendelErr. Saving output to a file should happen outside the function calls.
batchChisqTest and batchFisherTest have snp.include arguments to run on individual SNPs. Using batchFisherTest with this argument is recommended to replace the deprecated assocTestFisherExact.
Changes in version 1.13.21:
assocRegression replaces assocTestRegression. Only one model is allowed per function call.
assocCoxPH replaces assocTestCPH. Output format is now similar to assocRegression.
exactHWE replaces gwasExactHWE.
assocRegression, assocCoxPH, and exactHWE include the option to select blocks of SNPs by index for easier parallelization.
scan.chromosome.filter is no longer an option; use setMissingGenotypes to filter data prior to running other functions.
Changes in version 1.13.9:
Add use.names argument to getGenotype and getGenotype selection
Add order=c(“file”, “selection”) argument to getGenotypeSelection
duplicateDiscordanceAcrossDatasets and dupDosageCorAcrossDatasets will not match on unmapped SNPs
Changes in version 1.13.8:
Changes in version 1.13.7:
Add dupDosageCorAcrossDatasets.
Add getGenotypeSelection method to MatrixGenotypeReader.
Changes in version 1.13.6:
Changes in version 1.13.3:
Changes in version 1.1.2 (2015-01-09):
Changes in version 1.1.1 (2014-11-04):
Added the function transposedata.
Updated the vignette file.
Updated the CITATION file.
Updated output of the core fuctions.
Updated documentation.
Changes in version 1.1.1:
Changes in version 1.4.0:
Changes in version 1.3.0-1.3.2:
NEW FEATURES
support the human genome “hg20”
add a new function
hlaGDS2Geno() to support SNP GDS files (in the
R/Bioconductor package SNPRelate)
hlaReport() outputs text with markdown format
SIGNIFICANT USER-VISIBLE CHANGES
optimize the calculation of hamming distance using SSE2 and hardware POPCNT instructions if available
hardware POPCNT: 2.4x speedup for large-scale data, compared to the implementation in v1.2.4
SSE2 popcount implementation: 1.5x speedup for large-scale data, compared to the implementation in v1.2.4
BUG FIXES
bug fixes on big-endian machines (like Solaris SPARC, Apple PowerPC)
minor fix on random sampling from discrete uniform distribution
bug fix if ‘requireNamespace(“HIBAG”)’ instead of ‘require(HIBAG)’ is called from other packages
Changes in version 1.1.3:
Modified all bplapply calls
Moved BiocGenerics and rSFFreader to Imports
Changes in version 1.11.4:
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG FIXES
Changes in version 1.11.3:
BUG FIXES
Changes in version 1.11.1:
NEW FEATURES
BUG FIXES
Changes in version 1.9.1:
Updated to HPA version 13 <2014-11-15 Sat>
Use BiocStyle for vignette <2014-11-15 Sat>
Changes in version 1.7.1:
Changes in version 0.9.1 (2015-02-25):
Changes in version 0.9.0 (2014-10-13):
1.0.0: The first version caintains basically the functios and routines usesd to obtain the results of “Soerensen, T., Baumgart, S., Durek, P., Gruetzkau, A. and Haeupl, T. immunoClust - an automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets. Cytometry A (accepted).” CHANGES: * The code was cleaned and modified in the C-binding calls to make it runable on R 3.1.2. * A bug in the cell.hclust function was fixed, which does not effect the general results but lead to minor differences in concrete numbers. 0.99.7:
NEW FEATURES
Changes in version 0.99.6:
BUG FIXES
Changes in version 0.99.5:
BUG FIXES
Changes in version 0.99.4:
BUG FIXES
Changes in version 0.99.3:
BUG FIXES
Changes in version 0.99.2:
BUG FIXES
Changes in version 0.99.1:
BUG FIXES
Changes in version 1.7.1:
Notes
Changes in version 2.2.0:
NEW FEATURES.).
Add coercion methods from Hits to CompressedIntegerList, to PartitioningByEnd, and to Partitioning.
SIGNIFICANT USER-VISIBLE CHANGES ‘algorithm’ ‘minoverlap=0’, zero-width ranges are interpreted as insertion points and are considered to overlap with ranges that contain them. This is the 1st situation where using ‘algorithm=”nclist”’ or ‘algorithm=”intervaltree”’ produces different output. - When using ‘select=”arbitrary”’, the new algorithm will generally not select the same hits as the old algorithm. This is the 2nd situation where using ‘algorithm=”nclist”’ or ‘algorithm=”intervaltree”’ produces different output. - When using the old interval tree algorithm, ‘maxgap’ has a special meaning if ‘type’ is “start”, “end”, or “within”. This is not yet the case with the new algorithm. That feature seems somewhat useful though so maybe the new algorithm should also support it? Anyway, this is the 3rd situation where using ‘algorithm=”nclist”’ or ‘algorithm=”intervaltree”’ produces different output. - Objects preprocessed with NCList(), NCLists(), and GNCList() are serializable.
The RleViewsList() constructor function now reorders its ‘rleList’ argument so that its names match the names on the ‘rangesList’ argument.
Minor changes to breakInChunks(): - Add ‘nchunk’ arg. - Now returns a PartitioningByEnd instead of a PartitioningByWidth object. - Now accepts ‘chunksize’ of 0 if ‘totalsize’ is 0.
300x speedup or more when doing unique() on a CompressedRleList object.
20x speedup or more when doing unlist() on a SimpleRleList object.
Moved the RleTricks.Rnw vignette to the S4Vectors package.
DEPRECATED AND DEFUNCT IntervalTree and IntervalForest objects.
seqapply(), seqby(), seqsplit(), etc are now defunct (were deprecated in IRanges 2.0.0).
Removed map(), pmap(), and splitAsListReturnedClass() (were defunct in IRanges 2.0.0).
Removed ‘with.mapping’ argunment from reduce() methods (was defunct in IRanges 2.0.0).
BUG FIXES
findOverlaps,Vector,missing method now accepts extra arguments via … so for example one can specify ‘ignore.strand=TRUE’ when calling it on a GRanges object (before that, ‘findOverlaps(gr, ignore.strand=TRUE)’ would fail).
PartitioningByEnd() and PartitioningByWidth() constructors now check that, when ‘x’ is an integer vector, it cannot contain NAs or negative values.
Changes in version 1.13.0:
calcCumulativeProbXGreaterThanY() contributed by A. Stukalov, for calculating cummulative p-values with replicates
Bioconductor version increment
Changes
Changes in version 1.1.8:
new accessors selGridRow, selGridCol and fullModel for class ModelSelectionResult
change of naming of feature weights because of change in LiblineaR 1.94-2
GCC warnings in Linux removed
Changes in
Changes in
Changes in
check uniqueness of motifs in motif kernel
minor changes in help pages
change name of vignette Rnw to lowercase
minor changes in vignette
Changes in version 1.1.4:
Changes in version 1.1.3:
Changes in
Changes in version 1.1.1:
correction for cross validation with factor label
correction for storing prob model in kebabs model for kernlab
removal of clang warnings for unused functions
Changes in version 1.1.0:
Changes in version 1.9.3:
Changes in version 1.9.1:
Changes in version 3.24.0:
Limma review article (Ritchie et al, Nucleic Acids Research, 2015) is now published, and becomes the primary citation for limma. References in User’s Guide, help files and CITATION have been updated to refer to this article.
New function plotMD() for mean-difference plots. This will take over the functionality of the plotMA() function.
mdplot() has new arguments ‘columns’ and ‘main’.
Arguments ‘pch’, ‘cex’ and ‘col’ of plotWithHighlights() renamed to ‘hi.pch’, ‘hi.cex’ and ‘hi.col’. Improved help page for plotWithHighlights().
plot() methods removed for EList, MAList and MArrayLM objects. Use plotMD() instead.
New function fry() provides a fast version of mroast() when there is little heteroscedasticity between genes.
Minor change to mroast() output so that FDR values are never smaller than p-values, even when mid-p-values are used.
camera(), roast(), mroast() and romer() now give a warning if any arguments found in … are not used.
romer() is now an S3 generic function. Speed improvements for romer() when the “mean” or “floormean” set statistics are used.
topGO() can now sort gene ontology results by several p-value columns at once, using the minimum of the columns. The default is now to sort results using all the p-value columns found in the results instead of just by the first column.
goana() has new arguments ‘plot’ and ‘covariate’. The plot argument allows users to view any estimated trend in the genewise significance values. The help files goana.Rd and goana.MArrayLM.Rd are consolidated into one file.
plotDensities() has a new argument ‘legend’, allowing user to reposition the legend.
voomWithQualityWeights() has a new argument ‘col’, allowing the barplot of sample weights to be colour-coded.
Improvements and bug fixes to plotMDS(). plotMDS now stores ‘axislabel’, depending on the method used to compute distances, and uses this to make more informative axis labels. plotMDS now traps problems when the distances are all zero or if one or more of the dimensions are degenerate. Also, a bug when gene.selection=”common” and top=nrow(x) has been fixed.
The arguments for predFCm() have been renamed. Old argument ‘VarRel’ replaced by logical argument ‘var.indep.of.fc’. Old argument ‘prop’ replaced by ‘all.de’. New argument ‘prop.true.null.method’ passes through method to propTrueNull().
vennDiagram() now fills circles with specified colors.
plotMA() now has a method for EListRaw objects.
voomWithQualityWeights() now stores the sample weights in the output EList object. The values stored in $weights are unchanged, they are still the combined observation and sample weights.
nec() and neqc() now remove the background Eb values if they exist in the EListRaw object.
Acknowledgements edited in User’s Guide.
fix URLs for a number of references in help pages.
Improvements to lowess C code.
When loading suggested packages within function calls, usages of require() have been converted to requireNamespace() wherever possible. Functions from suggested packages are called using `::’.
topTable() now gives an information error message if eBayes() or treat() have not already been run on the fitted model object.
genas() now gives an error message when applied to fitted model for which the coefficient correlations are gene-specific.
Fix a bug in the MAList method for plotDensities that was introduced with the use of NextMethod() in version 3.21.16.
Changes in version 0.99.4:
custom perl command was added to the methods setup and alignsequences bug fixes:
onLoad check added for: -> if “clustalo” is not in the PATH, a warning is raised -> if clustalo version is not 1.2.x, a warning is raised -> if XML:Simple and LWP modules for perl are not installed, a warning is raised
check for exit status of clustalo system call added
Changes in version 0.99.3:
alignSequences can now run in web mode. No clustalo is necessary but the limit is set to 2000 sequences and a email address is required. In addition, perl must be installed in the system
the newLowMACA constructor is now able to check all possible gene symbols, even if they are not protein coding genes or if they are not mapped in LowMACAAnnotation package
add a conversion from U (selenocystein) to A in amino acid sequences while creating the LowMACA object (‘newLowMACA’ function) in order to fix a problem with .Trident_Score function
modified check validity function in order to accept ‘auto’ in the bandwidth
‘protter’ method is now compatible with Windows OS
a check was added in newLowMACA constructor to prevent more than one pfam ID entry by the user
Changes in version 0.99.2:
modified ‘lfm’ method in order to accept different thresholds of p value or q value and conservation score
removed the output folder: -> now all plots can be evaluated on the graphical device -> clustalOmega output file is saved only if a path is provided either in ‘alignSequences’ method or ‘setup’ method
in ‘lmPlot’ if the mode is ‘gene’ and only one sequence is analyzed, domains are represented within the plot and no logo plot and trident score are visualized
the method ‘paths’ has been removed and all the options are now accessible through ‘lmParams’ method
Changes in version 1.3.2:
Changes in version 1.3.1:
Changes in version 1.9:
Added flexibility in formula choice for fitTimeSeries
Added readability in ssPermAnalysis
Fixed default in plotClassTimeSeries (include = c(“1”,…))
Added fitTimeSeries vignette
Removed interactiveDisplay to namespace - moved to suggests
Fixed ordering of MRtable,MRfulltable first four columns
modified df estimated through responsibilities
renamed fitMeta to fitLogNormal - a more appropriate name
Changes in version 1.3.5:
Changes in version 1.3.4:
Changes in version 1.3.3:
Changes in version 1.3.2:
Changed LC settings to explicitly include retcor arguments
Corrected LC bug on the PeakTable export when data files are stored into multiple subfolders
Changes in version 1.3.1:
Changed LC settings so that the retcor algorithm is passed correctly to the underlying XCMS function
Changed LC pipeline so that all user-defined settings are actually used
Changes in version 1.5.31 (2015-03-05):
NEW FEATURES
Added support for both forward and reverse RNA-Seq library preparation protocol. Thanks to Ben Elsworth, Garvan Institute of Medical Research, Syndey, Australia.
Added Reads per Gene Model length (rpgm) measurement, where gene model length is either the sum of exon lengths or the gene length (depending on count.type argument).
BUG FIXES
Changes in version 1.5.21 (2015-01-09):
NEW FEATURES
BUG FIXES
Changes in version 1.5.15 (2014-12-22):
NEW FEATURES
BUG FIXES
Introduced a (hopefully robust) fix for constant changes in Ensembl schema for human GRC37 (hg19). It increases annotation retrieval time though
Fixed problem when input counts are a data.frame and count.type in exon, introduced during package upgrades. Thanks to Ben Elsworth, Garvan Institute of Medical Research, Austria.
Replaced “==” with all.equal while checking if the sum of weights is one when meta.p=”weight”. Of course this is the correct way to compare. Thanks to Ben Elsworth, Garvan Institute of Medical Research, Syndey, Australia.
Fixed problem related to a bug in the current version of edgeR GLM and the usage of … in glmFit.
Changes in version 1.5.2 (2014-12-30):
NEW FEATURES
BUG FIXES
Changes in version 1.5.1 (2014-10-31):
NEW FEATURES
BUG FIXES
Changes in version 1.1.10:
Changes in version 1.1.9:
Changes in version 1.1.5:
Changes in version 1.1.4:
BUG FIXES
Changes in version 1.1.3:
Changes in version 1.1.2:
Changes in version 1.13:
read.450k.exp has support for argument base when targets is supplied. Thanks to Brent Pedersen bpederse@gmail.com for noticing this and providing an initial fix.
changed the default behaviour of read.450k.exp. If called using a targets argument created by read.450k.sheet, you should not also give it a base argument (which was always superfluous).
Some NAMESPACE imports fixes.
getGenomicRatioSetFromGEO added to read directly from GEO and create a GenomicsRatioSet. Thanks Tim Triche for writing the original function.
makeGenomicRatioSetFromMatrix added. This function turns a matrix into a GenomicRatioSet. The 450K feature IDs need to be supplied or in the rownames of the matrix.
makeGenomicRatioSetFromMatrix added to convert matrices to GenomicRatioSets. This can be useful for reading in files with beta values and turning into object that can be directly passed to bumphunter and blockFinder.
readGEORawFile added to read raw intensity files provided as Supplementary Material on GEO. The files include the unmethylated and methylated signals. The new function returns a GenomicMethylSet which permits you to seamlessly apply minfi preprocessing functions.
readTCGA is wrapper for makeGenomicRatioSetFromMatrix that reads in files in the TCGA format. The function is very specific to this format.
Minor coding fixes including some NAMESPACE issues, missing pData<- methods, replace require() with requireNamespace().
cpgCollapse now works for GenomicRatioSets since it no longer attempts to summarize CN data when passed a GenomicRatioSet.
estimateCellCounts now works on only 2 cell types.
Various NAMESPACE fixes.
the gaphunter function by Shan Andrews has been added. We welcome Shan as a contributing author.
Changes in version 1.1.10:
Changes in version 1.1.3:
Changes in version 1.1.2:
Changes in version 0.99.4:
NEW FEATURES
Changes in version 1.1.5:
Changes in version 1.1.1:
Changes in version 1.11.8:
NEW FEATURES
BUG FIXES
Changes in version 1.11.7:
NEW FEATURES
BUG FIXES
Changes in version 1.11.6:
NEW FEATURES
BUG FIXES
Changes in version 1.11.5:
NEW FEATURES
BUG FIXES
Changes in version 1.11.4:
NEW FEATURES
BUG FIXES
Changes in version 1.11.3:
NEW FEATURES
BUG FIXES
Changes in version 1.11.2:
NEW FEATURES
export function highlightCol
add function motifCircos
BUG FIXES
Changes in version 1.11.1:
NEW FEATURES
BUG FIXES
Changes in version 1.0.0:
Changes in version 1.1.2:
Changes in version 1.15.18:
fix failing test_MSnExp::readMSData unit test on Windows i386 (@.cache$size being different on that arch) [2015-04-14 Tue]
merge @vladpetyuk PR #50 fix of combine features bug [2015-04-14 Tue]
Changes in version 1.15.17:
Changes in version 1.15.16:
Changes in version 1.15.15:
Changes in version 1.15.14:
Changes in version 1.15.13:
improve nbavg imputation description and add example [2015-03-22 Sun]
reduce compareSpectra example timing [2015-03-30 Mon]
Changes in version 1.15.12:
Changes in version 1.15.11:
Changes in version 1.15.10:
update compareSpectra man [2015-03-19 Thu]
ExpressionSet <-> MSnSet coercion [2015-03-19 Thu]
Changes in version 1.15.9:
Changes in version 1.15.8:
Changes in version 1.15.7:
Importing ProtGenerics [2015-02-28 Sat]
selective import of MALDIquant [2015-03-02 Mon]
Changes in version 1.15.6:
add intensity column to the calculateFragments output; closes #47;1 [2015-02-02 Mon]
add method argument to calculateFragments to allow the user choosing the highest/closest peak or all peaks in the tolerance range; closes #47;2 [2015-02-09 Mon]
add neutralLoss argument to calculateFragments and calculate loss of water and ammonia; closes #47:3 [2015-02-19 Thu]
new imputation methods via imputeLCMD and norm [2015-02-09 Mon]
vignette updates [2015-02-09 Mon]
imputation unit test [2015-02-24 Tue]
Changes in version 1.15.5:
update dependency to mzID >= 1.5.2 [2015-01-28 Wed]
rewrite addIdentificationData and change its signature [2015-01-28 Wed]
add methods addIdentificationData which work on MSnExp and MSnSets using filenames (characters), mzID objects and data.frames; see #42; closes #45; [2015-01-28 Wed]
add a section about MSmaps in the vignette [2015-02-02 Mon]
MSmap has a new zeroIsNA argument to set all 0 values of the map to NA. This simplifies the resulting plot3D figure. [2015-02-02 Mon]
Changes in version 1.15.4:
partly rewrite readMgfData [2015-01-19 Mon]
Typo in addIdentification data man [2015-01-20 Tue]
use Biocstyle [2015-01-23 Fri]
replace require with requireNamespace [2015-01-23 Fri]
Changes in version 1.15.3:
plot,Spectrum2,character to add fragment ions based on peptide sequence [2014-11-20 Thu]
update vignette with above [2014-11-20 Thu]
comment parallel code in quantify man [2015-01-09 Fri]
Changes in version 1.15.2:
merged sgibb’s pull request exporting overloaded methods as well [2014-11-02 Sun]
updated MSnSet validity, checking that exprs(.) is a matrix [2014-11-12 Wed]
fix error (missing header extraction) is MSmap example [2014-11-18 Tue]
Changes in version 1.15.1:
Changes in version 1.15.0:
Changes in version 1.1.6:
Added explicit mc.cores argument for “Grid” type of optimization
Fix of trimming to basename on POSIX
Changes in version 1.1.5:
Changes in version 1.1.4:
Changes in version 1.1.3:
Changes in version 1.1.2:
id_quality and evaluate_filter may have multiple values for the level argument. By default it is all three: “PSM”, “peptide” and “accession”. The return value for both methods is switched to matrices.
added Laurent Gatto as a contributor
Changes in version 1.1.1:
fix mishandling PSM
use mzR::psms generic
Changes in version 1.1.0:
Changes in version 1.5.3:
Changes in version 2.1.12:
Remove superfluous BiocGenerics in Suggests [2015-03-01 Sun]
Merged KK’s Makefile to generate pwiz lib for windows [2015-03-01 Sun]
Changes in version 2.1.11:
Changes in version 2.1.10:
Add instrumentInfo() and runInfo() for CDF backend (closes issue #22)
Add precompiled libpwiz.a to reduce compile time on Windows (closes issue #21), thanks to KK
Changes in version 2.1.9:
Changes in version 2.1.8:
Changes in version 2.1.7:
Fix score segfault (see issue #18) and remove usage of ListBuilder.
Update unit test to reflext new score code.
Changes in version 2.1.6:
Changes in version 2.1.5:
don’t print ‘1’ to the console when calling get3Dmap [2015-01-29 Thu]
add sequence length in psms output (closes issue #19) [2015-02-04 Wed]
Changes in version 2.1.4:
Changes in version 2.1.1:
0.99.5: First Bioconductor-devel release.
Changes in version 1.3.1:
Changes in version 1.3.8:
Changes in version 1.3.7:
Changes in version 1.3.6:
Changes in version 1.3.5:
Changes in version 1.3.4:
Changes in version 1.3.3:
Changes in version 1.3.2:
Changes in version 1.3.1:
Added a requirement that each treatment group have at least two observations.
Set a minimum p-value for the Beta approximation so that it never returns a value of zero
Changes in version 1.32:
USER VISIBLE CHANGES
Fixed vignette
Added initial support to Generic Arrays
Using BiocGenerics definition of normalize
Changes in version 1.7.1:
NEW FEATURES
mcia will return pairwise RV coefficient in the “$mcoa”
updated reference
Changes in version 1.1.1 (2015-03-13): 0.6.13:
Changes in version 0.6.12:
Changes in version 0.6.11:
Changes in version 0.6.10:
plotting helper functions [2015-02-28 Sat]
fixed peptide grouping [2015-02-28 Sat]
Changes in version 0.6.9:
Fixing junction peptides splitting to support peptides reaching > 2 exons [2015-02-27 Fri]
supporting more protein coding biotypes [2015-02-27 Fri]
rewrite and simplify proteinCoverage; closes #19 [2015-02-27 Fri]
Changes in version 0.6.8:
Changes in version 0.6.7:
Changes in version 0.6.6:
Changes in version 0.6.5:
see also mapping vignette in ?mapToGenome [2015-02-20 Fri]
calculateHeavyLabels, isCleaved, proteotypic and proteinCoverage are is now a function [2015-02-20 Fri]
added accessors to Pbase:::pplot() and update Pbase-data vignette accordingly [2015-02-21 Sat]
Changes in version 0.6.4:
typos in man [2015-02-19 Thu]
Added use.names argument ot etrid2gel [2015-02-19 Thu]
mapToGenome,Proteins,GRangesList (remove GRanges) using names for 1-to-many mapping and document in mapping vignette [2015-02-19 Thu]
Changes in version 0.6.3:
new fig in Pbase-data vignette [2015-02-14 Sat]
new section for pmapToGenome in mapping vignette [2015-02-14 Sat]
Changes in version 0.6.2:
Add uniprot release to p metadata [2015-02-14 Sat]
added a metadata update method [2015-02-14 Sat]
Changes in version 0.6.1:
Changes in version 0.6.0:
fixed typos in vigs [2015-02-12 Thu]
new etrid2grl function to convert Ensembl transcript identifiers to GRangesList objects [2015-02-13 Fri]
initial mapToGenome function [2015-02-13 Fri]
regenerated p data using latest UniProt release and added acols(p)$ENST [2015-02-13 Fri]
Changes in version 1.32:
BUG FIXES
USER VISIBLE CHANGES
Changes in version 2.1.3:
NEW FUNCTIONALITY
Box-Cox transformation is applied when needed for the continues data. Transformation values are shown in output functions. Genotype effects are converted back into original scale if transformation was applied.
New statistical method is implemented for the categorical data - Logistic Regression.
New function is created boxplotSexGenotypeBatchAdjusted() that allows to evaluate Batch effect.
Major architectural changes: classes PhenList and PhenTestResult are S4 classes now. Different new methods are provided for the classes.
PhenTestResult object contains dataset analysedDataset() that was used for the analysis including original values, transformed values (if transformation has been applied) and values adjusted for batch effect.
COMPATIBILITY ISSUES
Changes in version 1.5.10:
Changes in version 1.5.7:
NEW FEATURES
1.2.3: change URL of example chromosome 22 sequence dataset / do not test internet-connectivity-dependent stuff during check
1.2.2: bug fix in fragment start position simulation with positional bias
1.2.1: major refactor: - reduced number of arguments for wrapper functions (simulate_experiment and simulate_experiment_countmat) - shortened source code in wrapper functions by adding several internal helper functions
1.2.1: several new features added: - GC bias in expression - empirical fragment length distribution model available - positional bias in fragmentation step - empirical error models available - custom library size factors available - simulate_experiment_empirical function added as quick way to simulate an experiment with abundances derived from a data set
Changes in version 1.7.1:
Changes in version 1.4.1:
Changes in version 1.7.13:
Changes in version 1.7.12:
Changes in version 1.7.11:
Changes in version 1.7.10:
Changes in version 1.7.9:
updated tl vignette [2015-04-02 Thu]
depending on latest (1.5.8) pRolocdata [2015-04-02 Thu]
Changes in version 1.7.8:
updating tl vig [2015-04-02 Thu]
update getParams documentation [2015-04-02 Thu]
Changes in version 1.7.7:
Changes in version 1.7.6:
added the theta inductive transfer infrastructure [2015-02-05 Thu]
theta vignette stub [2015-02-06 Fri]
rename getClasses to getMarkerClasses [2015-02-06 Fri]
added the infrastructure to create GO MSnSet [2015-02-07 Sat]
Fixed ml vignette [2015-02-16 Mon]
new filterZeroRows function [2015-03-10 Tue]
hpa data section [2015-03-10 Tue]
theta sections [2015-03-10 Tue]
Changes in version 1.7.5:
Changes in version 1.7.4:
Changes in version 1.7.3:
use Biocstyle [2015-01-23 Fri]
replace library/require by requireNamespace [2015-01-23 Fri]
Changes in version 1.7.2:
added t-SNE method to plot2D [2015-01-14 Wed]
Updated NAMESPACE imports [2015-01-14 Wed]
Changes in version 1.7.1:
updated vignettes with markers.orig [2014-10-30 Thu]
updated ml tests [2014-10-30 Thu]
Changes in version 1.7.0:
Changes in version 1.1.5:
Changes in version 1.1.4:
Changes in version 1.1.3:
Changes in version 1.1.2:
Changes in version 1.1.1:
Update README with uptodate installation instructions [2014-10-14 Tue]
handling and filtering missing value in input data [2014-10-21 Tue]
Changes in version 1.3.2:
Changes in version 1.3.1:
Update the function labelRatio
Update the vignette
Changes in version 0.99.3:
Changes in version 0.99.2:
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 1.5.1:
Changes in version 1.2.4 (2015-01-21):
OTHER
Changes in version 1.2.3 (2015-01-20):
BUG FIXES
Changes in version 1.2.2 (2014-12-23):
IMPROVEMENTS
Changes in version 1.2.1 (2014-11-01):
IMPROVEMENTS
add an asterisk in the noise measure to clarify it’s not a regular standard deviation or variance, but first scaled with the mean (so that the mean is 1.0 and the relationship holds between variance and 1/N, where N is the average number of reads per bins)
clarify the use of log2/sqrt transformation in segmentBins()
Changes in version 2.20:
USER VISIBLE CHANGES
BUG FIXES
Changes in version 0.99.0:
First release of the QuartPAC package.
Currently supports the iPAC, GraphPAC and SpacePAC packages when extending clustering results to quarternary data.
Changes in version 1.8.0:
PUBLICATION
NEW FEATURES
Changes in version 1.99:
This update of the qvalue package includes
removal of tcltk usage
the use of ggplot2 in the plotting functions
an updated vignette
vectorizing sections of the code
function name changes
inclusion of local FDR estimation
2015.02.1:
Changes in version 1.13.1 (2015-01-26):
fixed the bugs in function “export3Cseq2bedGraph”
fixed the bugs in function “getViewpoint”
fixed the bugs in function “export3CseqRawReads2bedGraph”
added “mm10” and “rn5” genomes into the package
Changes in version 1.7.9:
NEW FEATURES
Changes in version 1.11.9:
Changes in version 1.11.8:
Changes in version 1.11.7:
Changes in version 1.11.6:
Changes in version 1.11.5:
Changes in version 1.11.2:
Changes in version 1.11.1:
Changes in version 1.15.0:
Improved app reliability.
Implemented new compatibility checks for call-back functions.
Fix a client-server issue related with some MS-Windows specifications.
Changes in version 1.1.9:
NEW FEATURES
Introduced renderReport() which creates a simple exploratory report for any set of genomic regions. It allows the user to further customize the report by using a child file.
You can now use the ‘output_format’ advanced parameter on both renderReport() and derfinderReport() to output a PDF file instead of an HTML file. The interactive tables are lost and only the top 20 rows are shown.
Changes in version 1.1.8:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 1.1.7:
NEW FEATURES
Changes in version 1.1.3:
BUG FIXES
Changes in version 2015-3-27:
Changes in version 0.99.5:
Changes in version 0.99.4:
Changes in version 0.99.15:
BUG FIXES
Changes in version 0.99.12:
NEW FEATURES
Changes in version 0.99.11:
BUG FIXES
bugfix in ProcessAll cardinality message.
Error catching around PCA.
Heatmap genelist now respects Annote_Filter file when LIMIT$HARD.
Cleaned up warnings when no rows for HMA.
Bugfix in PCA regarding non-negative definite covariance from princomp’s eigen: replaced all instances with prcomp().
Changes in version 0.99.10:
BUG FIXES
Changes in version 0.99.4:
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 2.12.0:
NEW FEATURES
Filenames are expanded with normalizePaths.
New function h5set_extent implemented.
New low level function H5Sset_extent_simple implemented.
BUG FIXES
1.9.1: 1. Added citation information. 2. The identification of investigation files now avoids editor backup files (ignoring files like “i_Investigation~”) 3. Fixed issue where the investigation file wasn’t fully read, due to the number of columns in higher rows being greater than the first five rows (as used by read.table) 4. Moved inst/doc to vignettes folder as required since R 3.1.0 5. Imported packages in Depends 6. Removed ‘library’ or ‘require’ calls to packages already attached by Depends. 7. Fixed no visible binding for global variable.
Changes in version 0.99.4:
NEW FEATURES
Changes in version 0.99.8 (2015-04-12):
BUG FIXES
Changes in version 0.99.7 (2015-04-06):
BUG FIXES
Changes in version 0.99.5 (2015-04-06):
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.4:
NEW FEATURES
BUG FIXES
Bug fixed: Max sample size for distribution based sample size estimation;
Bug fixed: Keep consistent for all function names;
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.3 (2014-11-23):
SIGNIFICANT USER-VISIBLE CHANGES
New parameter: countFilterInRawDistribution, selectedGeneFilterByCount;
Other improvement based on the comments from Bioconductor reviewer;
Changes in version 0.99.2:
SIGNIFICANT USER-VISIBLE CHANGES
The vignette was switched to a BiocStyle;
Other improvement based on the comments from Bioconductor reviewer;
Changes in version 0.99.1 (2014-10-19):
SIGNIFICANT USER-VISIBLE CHANGES
Parameter was used to determine the power of genes below minAveCount;
Some recommendations from BiocCheck were improved;
Changes in version 0.99.0 (2014-10-16):
SIGNIFICANT USER-VISIBLE CHANGES
Changes in version 0.99.22:
Changes in version 0.99.20:
Changes in version 0.99.19:
Fixed a bug in the computation of surrogate variables (SVA) that did not take into account other adjustment variables in the model (compared to the null model)
Updated locus profiles to work with the latest version of Gviz
Differential methylation reports now contain information on group sizes
Included plots of number of sites vs coverage percentiles for each sample in the dataset (rnb.plot.num.sites.covg)
Bisulfite-seq QC reports now contain an additional section with summary statistics and plots when the coverage histogram plots are enabled
Changes in version 0.99.18:
Implementation of class constructors (the S4 constructors are not available anymore)
Analyses can now be started from an RnBSet which is stored on the hard drive (using save.rnb.set) via the rnb.set.dir data type
New IDAT loading routine, based on the illuminaio package
Multiple fixes in wrappers for wateRmelon normalization methods
Fixed the RefFreeEWAS wrapper
Updated the Houseman, 2012 reference-based method implementation
RnBSets now know the version with which they were created
Various other bugfixes and improvements to reports and documentation
Changes in version 0.99.17:
Consistency issues with Bioconductor 3.0 fixed
Fixed a bug relating to no coverage masking being conducted for sequencing data
Various other bugfixes
Changes in version 0.99.16:
Enhanced XML-based analysis though the tag preanalysis.script
Optimized loading of the sequencing data sets
Enhanced region profiles plots. Added region site distribution plots
Locus profiles can now be generated in the exploratory report for regions specified in custom bed files and for genes listed as gene symbols
Improved cell type heterogeneity inference (no cell types excluded anymore)
Added more support for paired differential methylation with limma
Some functions were renamed: merge.samples->mergeSamples, add.pheno->addPheno, add.region.subsegments->addRegionSubsegments, and all functions operating on Report
Added helper classes for submitting RnBeads to a scientific compute cluster. Current implementation includes Sun Grid Engine
The default pipeline now uses ff functionality and saves intermediate objects into the report directory
Minor bugfixes
Changes in version 0.99.15:
Restructuring of the pipeline modules: ** the loading module has been renamed to import ** the prefiltering,normalization and postfiltering modules have been summarized in a new module: preprocessing ** the batch and profiles modules have been summarized in a new module for exploratory analysis ** the export module has been renamed to tracks and tables ** corresponding option names have been changed ** see the overview figure on the website or the vignette for a quick overview on the new module structure
Multiple RnBSets can now be concatenated with the add() function
Multiple samples in an RnBSet can be merged using the merge.samples() function
Gender prediction can be performed on Infinium 450k datasets
Minor updates on covariate adjustment
Updates on tissue heterogeneity estimation
Calling differentially methylated sites with RefFreeEWAS now supports paired design
Multiple minor bugfixes and performance improvements
Vignette and documentation updates
Changes in version 0.99.13:
Added new module on annotation inference
Added correction for cell type heterogeneity
Added SVA functionality
Minor bugfixes
Updates to the vignette and other documentation
Changes in version 0.99.12:
Support Bismark coverage file loading
Enhanced documentation and logging of loading steps
Minor bugfixes
Updates to the vignette and other documentation RnBeads 0.99.11
Accommodate data packages for individual genomes
Performance: disk space usage when using disk dumping, options for subsetting sites when computing distance matrices for clustering, PCA and MDS
Region subsegmentation
The default method for differential methylation p-values is limma
Changes in version 0.99.10:
Performance improvements
Option to keep big matrices on the hard drive rather than main memory
Restructuring of the filtering modules. Parts of the filtering steps are executed before normalization others afterwards
Improvements in normalization: more methods supported
Cosmetic changes to some of the plots
Changes in version 0.99.9:
Bugfixes in paired analysis
Usability of bisulfite sequencing
Changes in version 0.99.8:
New normalization methods integrated
Improved arguments to rnb.run.analysis
Improved parsing of the sample annotation table
Paired analysis (testing stage)
Webservice installed
Multiple bugfixes
Changes in version 0.99.7:
Support for background subtraction and BMIQ normalization of Infinium 450k data
Support for differential methylation analysis on all pairs of sample groups
Changes in version 0.99.6:
Locus Profiles
Support for parallel computing
Changes in version 0.99.0:
Changes in version 1.3.1:
Changes in version 1.2:
NEW FEATURES
Study design metadata system (group ID, strand, etc) added
Statistics for trimming step added
Per sample mean quality box plot added
Per cycle mean quality Principal Component Analysis (PCA) plot added
Overrepresented sequencing reads plot added
USER VISIBLE CHANGES
RqcResultSet class stores data as frequency tables
BPPARAM argument added to rqc and rqcQA functions
BUG FIXES
Memory usage improved
Input file validation system
Rqc does not depend on X11 to generate plots
Rqc’s reporter can generate plots for more than 10 files
Fixed bug related with reshape2 dependency
Fixed bug related with table function
Changes in version 1.19:
SIGNIFICANT USER-VISIBLE CHANGES
FaFile accepts a distinct index file
Support for cigars > 32767 characters
Mate pairs use pos and mpos values calculated modulo target length for pairing, facilitating some representations of mates on circular chromosomes.
scanBam no longer translates mapq ‘255’ to ‘NA’
BUG FIXES
segfault on file iteration, introduced in 1.19.35, fixed in 1.19.44
scanBam correctly parses ‘=’ and ‘X’
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 1.1:
Corrected typo in vignette
RUV* methods for matrix now support log data
Changes in version 1.7.1-1.7.5:
bug fix in getting genotypes if position > 2^31
add an option ‘ignore.chr.prefix’ to the function ‘seqVCF2GDS’
‘seqVCF2GDS’ ignores the INFO or FORMAT variables if they are not defined ahead
a new action ‘push+set’ in the function ‘seqSetFilter’
bug fix if ‘requireNamespace(“SeqArray”)’ is called from other packages
Changes in version 1.5.1:
Use existing isSNV generic from VariantAnnotation instead of redefining
Use BiocStyle for vignette
Changes in version 1.2.0:
Renamed class TxVariants to SGVariants
Renamed class TxVariantCounts to SGVariantCounts
Renamed findTxVariants() to findSGVariants()
Renamed getTxVariantCounts() to getSGVariantCounts()
Parallelization is now controlled with a single cores argument
Argument max_complexity for predictTxFeatures() controls skipping of problematic regions
getBamInfo() is no longer run as part of analyzeFeatures()
getSGVariantCounts() now supports obtaining counts from BAM files
Bug fixes and other improvements
Changes in version 1.25:
SIGNIFICANT USER-VISIBLE CHANGES
srapply is defunct
readAligned() for BAM files is deprecated; use GenomicAlignments::readGAligned instead.
BUG FIXES
close opened files when parsing old bowtie, soap, and solexa export file formats.
Don’t allow R memory to be released prematurely when processing old bowtie file formats / creating external pointers.
writeFastq,FastqFile obeys ‘compress’ argument; mode must be specified by the caller (typically mode=”a”)
Changes in version 2.0.0:
Changes in version 0.99.3:
Changes in version 0.99.2:
Changes in version 0.99.1:
Changes in version 0.99.0:
Changes in version 1.1.0-1.1.11:
fix a bug in snpgdsVCF2GDS when ‘method=”biallelic.only”’
add ‘snpgdsVCF2GDS_R’ for the R implementation
fix a bug in ‘snpgdsBED2GDS’ if ‘family=TRUE’
‘snpgdsGDS2BED’ allows the file name of GDS
improve ‘snpgdsSlidingWindow’
add an option ‘ignore.chr.prefix’ to the function ‘snpgdsVCF2GDS’
a new function ‘snpgdsHWE’
v1.1.5: add ‘Fst estimation’ to the vignette
v1.1.6: bug fix if ‘requireNamespace(“SNPRelate”)’ is called from other packages
v1.1.7: snpgdsPCA uses ‘DSPEVX’ to compute eigenvalues and eigenvectors instead of ‘DSPEV’ if top eigenvalues are required only (significant improvement on computing speed)
v1.1.8: the original Rnw vignette is replaced by a R Markdown vignette
v1.1.9: a new function ‘snpgdsPED2GDS’
Changes in version 1.1.17:
USER UNVISIBLE CHANGES
Changes in version 1.1.16:
USER UNVISIBLE CHANGES
Changes in version 1.1.15:
USER UNVISIBLE CHANGES
added circle plots to specLSet plot method
added breaks argument in genSwathIonLib methode
Changes in version 1.1.14:
USER UNVISIBLE CHANGES
Changes in version 1.1.13:
USER VISIBLE CHANGES
Changes in version 1.1.12:
USER VISIBLE CHANGES
Changes in version 1.1.11:
USER VISIBLE CHANGES
modified default parameters of genSwathIonLib
add content to vignette
Changes in version 1.1.10:
USER VISIBLE CHANGES
Changes in version 1.1.9:
USER VISIBLE CHANGES
USER UNVISIBLE CHANGES
refactored merge.specLSet; merge by group_id
added unit test for merge.specLSet
Changes in version 1.1.8:
USER VISIBLE CHANGES
renamed annotateProteinID to annotate.protein_id
added graphics on plot.specLSet method
USER UNVISIBLE CHANGES
Changes in version 1.1.7:
USER VISIBLE CHANGES
introduce peakplot for bibliospec object
introduce LCMS map for bibliospec object
vignette cosmetics
Changes in version 1.1.6:
USER VISIBLE CHANGES
Changes in version 1.1.5:
USER VISIBLE CHANGES
specLSet merge function
work on specLSet summary method
specLSet merge function
work on specLSet summary method
Changes in version 1.1.4:
USER VISIBLE CHANGES
summary method of specLSet class
summary method of specLSet class
USER UNVISIBLE CHANGES
unit test for data containing no iRT peptides
unit test for data containing no iRT peptides
Changes in version 1.1.3:
USER VISIBLE CHANGES
renamed write.Spectronaut to write.spectronaut
write.spectronaut writes filename
added benchmark section in package vignette
renamed write.Spectronaut to write.spectronaut
write.spectronaut writes filename
added benchmark section in package vignette
Changes in version 1.1.2:
USER VISIBLE CHANGES
uses modSeq in group_id iff existing
uses modSeq in group_id iff existing
Changes in version 1.1.1:
USER VISIBLE CHANGES
streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for compatibility with peakView V2.0
streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for compatibility with peakView V2.0
Changes in version 1.21.11 (2015-03-22):
Changes in version 1.21.8 (2014-12-12):
Added fastq table to the database
Re-wrote getFastqInfo function
Fastq files can be downloaded by getFastqFile or getSRAfile
Added <dir2> to the fastq ftp addresses for SRR accessions over SRR999999
Changes in version 1.5.1:
NEW FEATURES
Changes in version 1.9.5:
Changes in version 1.9.4:
use biocstyle [2015-01-23 Fri]
use requireNamespace [2015-01-23 Fri]
Changes in version 1.9.3:
Changes in version 1.9.2:
Changes in version 1.9.1:
Deprecating synatperGUI [2014-11-10 Mon]
Directing questions to the Bioc support site [2014-11-10 Mon]
Changes in version 1.9.0:
Changes in version 1.24.0:
BUG FIXES
Changes in version 1.7.13:
fix bug in ‘.testBySamseq’.
fix bug in ‘simulateReadCounts’.
rewrite the R code.
‘fit0’ and ‘fit1’ arguments were changed to ‘full’ and ‘reduced’, ‘DESeq.test’ arguments were deleted.
‘voom’ in limma package wa added for DEG identification.
the ‘test.method’ for the comparison of paired two-group can be choosed from ‘edger’, ‘deseq’, ‘deseq2’, ‘bayseq’ and ‘voom’.
change the mode of expression of tcc$simulation$trueDEG. ‘0’ indicates a non-DEG and ‘1’ indicates a DEG, only ‘0’ and ‘1’ are used in this field.
‘groups’ argument in ‘plot.TCC’ function has changed to ‘group’.
Changes in version 1.5.0:
NEW FEATURES
searchSeq now works on DNAStringSet. The names in DNAStringSet will be used as seqname in SiteSet.
More user-friendly output in data.frame or GRanges from SiteSet, SiteSetList, et al.
reverseComplement works on XMatrix now.
faster implmentation of searchPairBSgenome
Changes in version 1.0.0:
Changes in version 1.3.4:
NEW FEATURES
BUG FIXES
Changes in version 1.3.3:
NEW FEATURES
BUG FIXES
Changes in version 1.3.2:
NEW FEATURES
BUG FIXES
Changes in version 1.3.1:
NEW FEATURES
add new function plotGRanges for quick view GRanges data
add ranges when importScore
BUG FIXES
Changes in version 1.3.1:
SIGNIFICANT USER-VISIBLE CHANGES
Updated the citation information.
Updated the help page of the package.
Changes in version 1.14.0:
NEW FEATURES
gVCF support: - missing END header written out with writeVcf() - expand() handles <NON_REF> ‘REF’ value
support ‘Type=Character’ in INFO header fields
add ‘row.names’ argument to expand()
add ‘Efficient Usage’ section to readVcf() man page
efficiency improvements to info(…, row.names=) - anyDuplicated() less expensive than any(duplicated()) - use row.names=FALSE when not needed, e.g., show()
add genotypeCodesToNucleotides()
add support for gvcf in isSNP family of functions
add VcfFile and VcfFileList classes
support ‘Type=Character’ of unspecified length (.)
add isDelins() from Robert Castelo
add makeVRangesFromGRanges() from Thomas Sandmann
MODIFICATIONS
‘ALT’ in expandedVCF output is DNAStringSet, not *List
remove .listCumsum() and .listCumsumShifted() helpers
add multiple INFO field unit test from Julian Gehring
add additional expand() unit tests
modify readVccfAsVRanges() to use ScanVcfParam() as the ‘param’; deprecate VRangesScanVcfParam
replace mapCoords() with mapToTranscripts()
change ‘CDSID’ output from integer to IntegerList in locateVariants() and predictCoding()
add readVcf,character,ANY,ANY; remove readVcf,character,ANY,ScanVcfParam
replace rowData() accessor with rowRanges()
replace ‘rowData’ argument with ‘rowRanges’ (construct SE, VCF classes)
BUG FIXES
readVcf() properly handles Seqinfo class as ‘genome’
allow ‘ignore.strand’ to pass through mapCoords()
writeVcf() no longer ignores rows with no genotype field
expand() properly handles - less than all INFO fields are selected - VCF has only one row - only one INFO column
don’t call path() on non-*File objects
split (relist) of VRanges now yields a CompressedVRangesList
predictCoding() now ignores zero-width ranges
Changes in version 1.4:
USER VISIBLE CHANGES
Genome sequence is not fixed to a specific human genome anymore and can be parametrized via a BSgenome package
The calculation of splice site strength on variants is now parametrized (the user can feed his/her own splice site matrices), optional and, by default, disabled because is quite computationally intensive and the user must be sure he/she wants to calculate it.
PhastConsDb and MafDb support has been updated. Older PhastConsDb and MafDb annotation packages will likely don’t work with this newer version of VariantFilering. The user must upgrade also those annotation packages.
Analysis functions unrelatedIndividuals(), autosomalRecessiveHomozygous(), etc. now can stream over the input VCF file to reduce the memory footprint.
Multiple single-sample VCF files are no longer supported. The user must provide always a single multi-sample VCF file.
Internally, the package uses now the VRanges-class to store variants and they can be now also retrieved in this container.
Indels are now annotated separtely as Insertions and Deletions. Added the annotation of Delins (deletion followed by insertion).
Added support for annotating non-SNVs using XtraSNPlocs.* packages.
Added support for associating BAM files to the resulting VariantFilteringResults object.
Added some basic variant visualization capabilities via de Gviz package and the support for associated BAM files.
Added HGVS annotations at genomic, coding and protein level.
Added annotations to Sequence Ontology terms.
Changed the display of VariantFilteringResults objects and added a summary() method that returns a data.frame tallying variants to feature annotations, which can be either BioC/VariantAnnotation features or Sequence Ontology features.
Updated the example VCF files of the CEU trio to include a smaller subset of variants but called with the latest version of the GATK pipeline. Added a subset of the corresponding BAM files with aligned reads around the 1Kb region of some of the called variants.
Integration of the IRanges/FilterRules mechanism into the filtering functionality, enabling the addition of user-specific filters.
BUG FIXES
Changes in version 1.43.3:
BUG FIXES
Changes in version 1.43.2:
BUG FIXES
Changes in version 1.43.1:
NEW FEATURE
Changes in version 3.2:
VERSION xps-1.27.1
The following packages are no longer in Bioconductor:
asmn, COPDSexualDimorphism, DNaseR, flowFlowJo, flowPhyto