Lal Claude Opus 4.6 commited on
Commit
36b7071
·
1 Parent(s): 4caf060

Add dataset statistics and fix loading code

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- 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>

Files changed (1) hide show
  1. README.md +40 -7
README.md CHANGED
@@ -10,10 +10,10 @@ size_categories:
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  - 1M<n<10M
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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.
@@ -21,15 +21,47 @@ This dataset provides a multi-class annotation of genomic regions across the hg3
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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 (e.g., EnhWk, Quies) |
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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 (training/validation/test) |
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  ## Usage
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@@ -38,9 +70,10 @@ import pandas as pd
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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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+
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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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+
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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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+
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+ ### Column Descriptions
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+
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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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+ ```