Shreshth Gandhi
commited on
Commit
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f0363f3
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Parent(s):
9195345
Update references to old name and add some tutorial links
Browse files
README.md
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@@ -66,12 +66,67 @@ offering broad applications across systems biology, drug discovery, and precisio
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```python
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from datasets import load_dataset
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# Load dataset in streaming mode
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ds = load_dataset("
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# View the first record
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next(ds.iter(1))
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```
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Please see the [Data Loading Tutorial](tutorials/loading_data.ipynb) for a walkthrough on using the data.
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## Dataset Features
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We provide multiple tables with the dataset including the main data (raw counts) in the `expression_data` table as well as
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various metadata in the `gene_metadata`,`sample_metadata`,`drug_metadata`,`cell_line_metadata`,`obs_metadata` tables.
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The main data can be downloaded as follows:
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```python
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from datasets import load_dataset
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tahoe_100m_ds = load_dataset("
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```
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Setting `stream=True` instantiates an `IterableDataset` and prevents needing to
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download the full dataset first. See [tutorial](tutorials/loading_data.ipynb) for an end-to-end example.
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### Gene Metadata
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```python
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gene_metadata = load_dataset("
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```
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| Column Name | Description |
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### Sample Metadata
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```python
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sample_metadata = load_dataset("
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```
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The sample_metadata has additional information for aggregate quality metrics for the sample as well as the concentration.
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### Drug Metadata
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```python
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drug_metadata = load_dataset("
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```
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The drug_metadata has additional information about each treatment.
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### Cell Line Metadata
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```python
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cell_line_metadata = load_dataset("
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```
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The cell-line metadata table has additional information about the key driver mutations for each cell line.
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```python
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from datasets import load_dataset
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# Load dataset in streaming mode
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ds = load_dataset("tahoebio/Tahoe-100m", streaming=True, split="train")
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# View the first record
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next(ds.iter(1))
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```
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### Tutorials
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Please refer to our tutorials for examples on using the data, accessing metadata tables and converting to/from the anndata format.
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Please see the [Data Loading Tutorial](tutorials/loading_data.ipynb) for a walkthrough on using the data.
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<table>
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<thead>
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<tr>
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<th>Notebook</th>
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<th>URL</th>
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<th>Colab</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>Loading the dataset from huggingface, accessing metadata, mapping to anndata</td>
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<td>
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<a href="https://huggingface.co/datasets/tahoebio/Tahoe-100M/blob/main/tutorials/loading_data.ipynb" target="_blank">
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Link
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</a>
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</td>
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<td>
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<a href="https://colab.research.google.com/github/huggingface/datasets/blob/main/datasets/tahoebio/Tahoe-100M/tutorials/loading_data.ipynb" target="_blank">
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<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open in Colab"/>
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</a>
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</td>
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</tr>
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</tbody>
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</table>
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### Community Resources
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Here are a links to few resources created by the community. We would love to feature additional tutorials from the community, if you have built something on top of
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Tahoe-100M, please let us know and we would love to feature your work.
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<table>
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<table>
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<thead>
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<tr>
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<th>Resource</th>
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<th>Contributor</th>
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<th>URL</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>Analysing Tahoe-100M with rapids-single-cell, scanpy and dask</td>
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<td>Theis Lab (@fabian_theis)</td>
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<td>
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<a href="https://theislab.github.io/vevo_Tahoe_100m_analysis/" target="_blank">
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Link
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</a>
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</td>
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</tr>
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</tbody>
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</table>
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## Dataset Features
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We provide multiple tables with the dataset including the main data (raw counts) in the `expression_data` table as well as
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various metadata in the `gene_metadata`,`sample_metadata`,`drug_metadata`,`cell_line_metadata`,`obs_metadata` tables.
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The main data can be downloaded as follows:
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```python
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from datasets import load_dataset
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tahoe_100m_ds = load_dataset("tahoebio/Tahoe-100M", streaming=True, split="train")
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```
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Setting `stream=True` instantiates an `IterableDataset` and prevents needing to
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download the full dataset first. See [tutorial](tutorials/loading_data.ipynb) for an end-to-end example.
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### Gene Metadata
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```python
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gene_metadata = load_dataset("taheobio/Tahoe-100M","gene_metadata", split="train")
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```
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| Column Name | Description |
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### Sample Metadata
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```python
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sample_metadata = load_dataset("tahoebio/Tahoe-100M","sample_metadata", split="train")
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```
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The sample_metadata has additional information for aggregate quality metrics for the sample as well as the concentration.
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### Drug Metadata
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```python
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drug_metadata = load_dataset("tahoebio/Tahoe-100M","drug_metadata", split="train")
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```
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The drug_metadata has additional information about each treatment.
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### Cell Line Metadata
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```python
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cell_line_metadata = load_dataset("tahoebio/Tahoe-100M","cell_line_metadata", split="train")
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```
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The cell-line metadata table has additional information about the key driver mutations for each cell line.
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