Cindy Ringhofer Brown, Brenda Elliott, Christine S Gipson, Jill Holmstrom, Devita Stallings
RN-to-BS Nursing Education Research: A Scoping Review
Nursing education perspectives
identifying impacted pathways important provides insights biology underlying conditions beyond detection differentially expressed genes importance analysis 100 pathway analysis methods developed thus far despite availability many methods challenging biomedical researchers learn properly perform pathway analysis first sheer number methods makes challenging learn choose correct method given experiment second computational methods require users savvy coding syntax comfortable commandline environments areas unfamiliar life scientists third learning tools computational methods typically implemented species ie human model organisms difficult perform pathway analysis species included many current pathway analysis tools finally existing pathway tools allow researchers combine compare contrast results different methods experiments hypothesis testing analysis purposes address challenges developed opensource r package consensus pathway analysis rcpa allows researchers conveniently 1 download process data ncbi geo 2 perform differential analysis using established techniques developed microarray sequencing data 3 perform gene set enrichment well topologybased pathway analysis using different methods seek answer different research hypotheses 4 combine methods datasets find consensus results 5 visualize analysis results explore significantly impacted pathways across multiple analyses protocol provides many example code snippets detailed explanations supports analysis 1000 species two pathway databases three differential analysis techniques eight pathway analysis tools six metaanalysis methods two consensus analysis techniques package freely available cran repository 2024 authors current protocols published wiley periodicals llc basic protocol 1 processing affymetrix microarrays basic protocol 2 processing agilent microarrays support protocol processing rna sequencing rnaseq data basic protocol 3 differential analysis microarray data affymetrix agilent basic protocol 4 differential analysis rnaseq data basic protocol 5 gene set enrichment analysis basic protocol 6 topologybased tb pathway analysis basic protocol 7 data integration visualization