Datasets:
| license: mit | |
| task_categories: | |
| - tabular-classification | |
| tags: | |
| - biology | |
| - genomics | |
| pretty_name: "ChromHMM fullstack annotation of the human genome" | |
| size_categories: | |
| - 1M<n<10M | |
| # human-chromhmm-fullstack-data | |
| ## Dataset Summary | |
| 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. | |
| ## Repository Content | |
| 1. `data.csv`: The main dataset stored in comma-separated tabular format. | |
| 2. `1_data.ipynb`: Jupyter notebook containing the preprocessing steps used to generate the `.csv` file. | |
| ## Dataset Structure | |
| - **Rows:** 5,809,104 | |
| - **Columns:** 7 | |
| ### Data Splits | |
| | Split | Count | | |
| |-------|-------| | |
| | train | 5,042,325 | | |
| | valid | 364,387 | | |
| | test | 402,392 | | |
| ### Chromatin States (16 classes) | |
| | State | Count | | |
| |-------|-------| | |
| | Quies | 1,485,576 | | |
| | Acet | 639,669 | | |
| | EnhA | 613,794 | | |
| | ReprPC | 610,147 | | |
| | Tx | 561,526 | | |
| | EnhWk | 543,113 | | |
| | HET | 521,161 | | |
| | TxWk | 254,518 | | |
| | TxEnh | 190,465 | | |
| | TxEx | 121,833 | | |
| | PromF | 88,429 | | |
| | GapArtf | 51,474 | | |
| | BivProm | 48,242 | | |
| | znf | 34,146 | | |
| | TSS | 24,402 | | |
| | DNase | 20,609 | | |
| ### Column Descriptions | |
| | Column | Type | Description | | |
| | :--- | :--- | :--- | | |
| | chrom | string | Chromosome name (e.g., chr1) | | |
| | start | int | Start coordinate of the genomic interval | | |
| | end | int | End coordinate of the genomic interval | | |
| | state | string | Chromatin state annotation (16 classes) | | |
| | interval_idx | int | Unique numerical index for the specific genomic interval | | |
| | enformer_split | string | Overlap with the data splits used for training the Enformer model | | |
| | split | string | Splits used for downstream modeling (train/valid/test) | | |
| ## Usage | |
| ```python | |
| import pandas as pd | |
| from huggingface_hub import hf_hub_download | |
| file_path = hf_hub_download( | |
| repo_id="Genentech/human-chromhmm-fullstack-data", | |
| filename="data.csv", | |
| repo_type="dataset" | |
| ) | |
| df = pd.read_csv(file_path) | |
| ``` | |