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--- |
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license: mit |
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task_categories: |
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- tabular-regression |
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tags: |
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- biology |
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- genomics |
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pretty_name: "Enformer Intervals" |
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size_categories: |
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- 10K<n<100K |
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--- |
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# enformer-data |
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## Dataset Summary |
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This dataset contains the specific genomic intervals used for training, validating, and testing the Enformer model, a deep learning architecture for predicting functional genomic tracks from DNA sequence. The intervals are provided for both human and mouse genomes. |
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- **Source Publication:** [Avsec, Ž., et al. "Effective gene expression prediction from sequence by integrating long-range interactions." Nat Methods 18, 1196–1203 (2021).](https://www.nature.com/articles/s41592-021-01252-x) |
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- **Genome Builds:** |
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- Human: hg38 |
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- Mouse: mm10 |
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## Repository Content |
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The repository includes two tab-separated values (TSV) files: |
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1. `human_intervals.tsv`: 38,171 genomic regions (excluding header). |
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2. `mouse_intervals.tsv`: 33,521 genomic regions (excluding header). |
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## Dataset Structure |
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### Data Fields |
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Both files follow a standard genomic interval format: |
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| Column | Type | Description | |
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| :--- | :--- | :--- | |
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| `chrom` | string | Chromosome identifier (e.g., `chr18`, `chr4`) | |
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| `start` | int | Start coordinate of the interval | |
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| `end` | int | End coordinate of the interval | |
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| `split` | string | Data partition assignment (`train`, `test`, or `val`) | |
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### Statistics |
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| File | Number of Regions | Genome Build | |
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| :--- | :--- | :--- | |
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| `human_intervals.tsv` | 38,171 | hg38 | |
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| `mouse_intervals.tsv` | 33,521 | mm10 | |
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## Usage |
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```python |
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from huggingface_hub import hf_hub_download |
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import pandas as pd |
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file_path = hf_hub_download(repo_id="Genentech/enformer-data", filename="human_intervals.tsv") |
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df_human = pd.read_csv(file_path, sep='\t') |
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file_path = hf_hub_download(repo_id="Genentech/enformer-data", filename="mouse_intervals.tsv") |
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df_mouse = pd.read_csv(file_path, sep='\t') |
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``` |
