Datasets:
Lal Claude Opus 4.6 commited on
Commit ·
36b7071
1
Parent(s): 4caf060
Add dataset statistics and fix loading code
Browse files- Add row count (5,809,104)
- Add data splits table (train/valid/test counts)
- Add chromatin state class distribution (16 states)
- Fix repo_type="dataset" missing from hf_hub_download
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
README.md
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---
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# human-chromhmm-fullstack
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## Dataset Summary
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This dataset provides a multi-class annotation of genomic regions across the hg38 genome. It is derived from the ChromHMM fullstack annotation (Vu & Ernst, 2022; https://doi.org/10.1186/s13059-021-02572-z). Genomic regions are classified into 16 states. The data is derived from https://public.hoffman2.idre.ucla.edu/ernst/2K9RS//full_stack/full_stack_annotation_public_release/hg38/hg38_genome_100_segments.bed.gz.
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## Repository Content
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1. `data.csv`: The main dataset stored in comma-separated tabular format.
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## Dataset Structure
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| Column | Type | Description |
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| :--- | :--- | :--- |
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| chrom | string | Chromosome name (e.g., chr1) |
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| start | int | Start coordinate of the genomic interval |
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| end | int | End coordinate of the genomic interval |
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| state | string | Chromatin state annotation (
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| interval_idx | int | Unique numerical index for the specific genomic interval |
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| enformer_split | string | Overlap with the data splits used for training the Enformer model |
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| split | string |Splits used for downstream modeling (
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## Usage
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from huggingface_hub import hf_hub_download
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file_path = hf_hub_download(
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repo_id="Genentech/human-chromhmm-fullstack-data",
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filename="data.csv"
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)
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df = pd.read_csv(file_path)
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```
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- 1M<n<10M
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---
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# human-chromhmm-fullstack-data
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## Dataset Summary
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This dataset provides a multi-class annotation of genomic regions across the hg38 genome. It is derived from the ChromHMM fullstack annotation (Vu & Ernst, 2022; https://doi.org/10.1186/s13059-021-02572-z). Genomic regions are classified into 16 chromatin states. The data is derived from https://public.hoffman2.idre.ucla.edu/ernst/2K9RS//full_stack/full_stack_annotation_public_release/hg38/hg38_genome_100_segments.bed.gz.
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## Repository Content
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1. `data.csv`: The main dataset stored in comma-separated tabular format.
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## Dataset Structure
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- **Rows:** 5,809,104
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- **Columns:** 7
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### Data Splits
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| Split | Count |
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|-------|-------|
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| train | 5,042,325 |
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| valid | 364,387 |
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| test | 402,392 |
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### Chromatin States (16 classes)
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| State | Count |
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|-------|-------|
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| Quies | 1,485,576 |
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| Acet | 639,669 |
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| EnhA | 613,794 |
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| ReprPC | 610,147 |
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| Tx | 561,526 |
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| EnhWk | 543,113 |
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| HET | 521,161 |
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| TxWk | 254,518 |
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| TxEnh | 190,465 |
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| TxEx | 121,833 |
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| PromF | 88,429 |
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| GapArtf | 51,474 |
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| BivProm | 48,242 |
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| znf | 34,146 |
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| TSS | 24,402 |
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| DNase | 20,609 |
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### Column Descriptions
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| Column | Type | Description |
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| :--- | :--- | :--- |
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| chrom | string | Chromosome name (e.g., chr1) |
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| start | int | Start coordinate of the genomic interval |
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| end | int | End coordinate of the genomic interval |
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| state | string | Chromatin state annotation (16 classes) |
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| interval_idx | int | Unique numerical index for the specific genomic interval |
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| enformer_split | string | Overlap with the data splits used for training the Enformer model |
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| split | string | Splits used for downstream modeling (train/valid/test) |
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## Usage
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from huggingface_hub import hf_hub_download
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file_path = hf_hub_download(
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repo_id="Genentech/human-chromhmm-fullstack-data",
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filename="data.csv",
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repo_type="dataset"
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)
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df = pd.read_csv(file_path)
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```
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