Datasets:

Genentech
/

human-chromhmm-fullstack-data

chrom stringclasses 22 values	start int64 9.59k 249M	end int64 10.6k 249M	state stringclasses 16 values	interval_idx int64 0 5.81M	enformer_split nullclasses 6 values	split stringclasses 3 values
chr1	792,508	793,532	GapArtf	0	null	train
chr1	793,908	794,932	Acet	1	null	train
chr1	794,408	795,432	EnhWk	2	null	train
chr1	795,908	796,932	Quies	3	null	train
chr1	798,608	799,632	GapArtf	4	null	train
chr1	800,908	801,932	Quies	5	null	train
chr1	801,808	802,832	TxWk	6	null	train
chr1	802,008	803,032	Tx	7	null	train
chr1	802,308	803,332	TxWk	8	null	train
chr1	803,008	804,032	Quies	9	null	train
chr1	803,608	804,632	TxWk	10	null	train
chr1	804,008	805,032	Quies	11	null	train
chr1	804,408	805,432	EnhA	12	null	train
chr1	804,608	805,632	Quies	13	null	train
chr1	804,908	805,932	TxWk	14	null	train
chr1	805,708	806,732	Quies	15	null	train
chr1	806,408	807,432	EnhA	16	null	train
chr1	806,608	807,632	Quies	17	null	train
chr1	806,808	807,832	EnhA	18	null	train
chr1	807,108	808,132	Quies	19	null	train
chr1	807,408	808,432	EnhWk	20	null	train
chr1	807,608	808,632	EnhWk	21	null	train
chr1	807,808	808,832	Acet	22	null	train
chr1	809,208	810,232	Quies	23	null	train
chr1	810,708	811,732	EnhWk	24	null	train
chr1	811,008	812,032	Tx	25	null	train
chr1	811,408	812,432	Quies	26	null	train
chr1	812,008	813,032	Tx	27	null	train
chr1	812,408	813,432	Tx	28	null	train
chr1	812,608	813,632	Tx	29	null	train
chr1	813,408	814,432	Quies	30	null	train
chr1	814,208	815,232	Tx	31	null	train
chr1	814,408	815,432	Tx	32	null	train
chr1	815,008	816,032	Quies	33	null	train
chr1	815,808	816,832	EnhWk	34	null	train
chr1	816,208	817,232	EnhA	35	null	train
chr1	816,408	817,432	EnhA	36	null	train
chr1	816,608	817,632	EnhA	37	null	train
chr1	816,808	817,832	PromF	38	null	train
chr1	817,008	818,032	EnhA	39	null	train
chr1	817,208	818,232	EnhWk	40	null	train
chr1	817,508	818,532	EnhA	41	null	train
chr1	817,808	818,832	EnhA	42	null	train
chr1	818,008	819,032	EnhWk	43	null	train
chr1	818,208	819,232	EnhA	44	null	train
chr1	818,508	819,532	TxEnh	45	null	train
chr1	818,808	819,832	TxEnh	46	null	train
chr1	819,108	820,132	Tx	47	null	train
chr1	819,508	820,532	TxEnh	48	null	train
chr1	821,108	822,132	Tx	49	null	train
chr1	822,808	823,832	TxEnh	50	null	train
chr1	823,208	824,232	Tx	51	null	train
chr1	823,608	824,632	Quies	52	null	train
chr1	824,008	825,032	Tx	53	null	train
chr1	824,208	825,232	Quies	54	null	train
chr1	824,408	825,432	Tx	55	null	train
chr1	824,608	825,632	Tx	56	null	train
chr1	824,808	825,832	Tx	57	null	train
chr1	825,008	826,032	Tx	58	null	train
chr1	825,208	826,232	TxEnh	59	null	train
chr1	825,408	826,432	PromF	60	null	train
chr1	825,608	826,632	TxEnh	61	null	train
chr1	825,808	826,832	PromF	62	null	train
chr1	826,008	827,032	EnhA	63	null	train
chr1	826,208	827,232	PromF	64	null	train
chr1	826,408	827,432	PromF	65	null	train
chr1	826,608	827,632	TSS	66	null	train
chr1	826,808	827,832	PromF	67	null	train
chr1	827,108	828,132	TSS	68	null	train
chr1	827,408	828,432	TSS	69	null	train
chr1	827,608	828,632	Quies	70	null	train
chr1	827,808	828,832	EnhA	71	null	train
chr1	828,008	829,032	EnhWk	72	null	train
chr1	828,308	829,332	EnhA	73	null	train
chr1	828,708	829,732	EnhWk	74	null	train
chr1	829,008	830,032	TxEnh	75	null	train
chr1	829,208	830,232	Tx	76	null	train
chr1	829,408	830,432	Tx	77	null	train
chr1	829,608	830,632	TxEnh	78	null	train
chr1	829,908	830,932	EnhA	79	null	train
chr1	830,208	831,232	Quies	80	null	train
chr1	830,408	831,432	EnhWk	81	null	train
chr1	830,608	831,632	EnhWk	82	null	train
chr1	830,808	831,832	EnhWk	83	null	train
chr1	831,008	832,032	TxEnh	84	null	train
chr1	831,208	832,232	Tx	85	null	train
chr1	831,408	832,432	Tx	86	null	train
chr1	831,608	832,632	Tx	87	null	train
chr1	831,908	832,932	TxEnh	88	null	train
chr1	832,608	833,632	TxWk	89	null	train
chr1	833,308	834,332	TxEnh	90	null	train
chr1	833,608	834,632	TxWk	91	null	train
chr1	833,808	834,832	TxWk	92	null	train
chr1	834,008	835,032	TxWk	93	null	train
chr1	834,208	835,232	Quies	94	null	train
chr1	834,408	835,432	TxWk	95	null	train
chr1	834,708	835,732	EnhWk	96	null	train
chr1	835,008	836,032	EnhWk	97	null	train
chr1	835,208	836,232	EnhWk	98	null	train
chr1	835,408	836,432	Quies	99	null	train

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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

data.csv: The main dataset stored in comma-separated tabular format.
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

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)

Downloads last month: 27

Size of downloaded dataset files:

284 MB

Size of the auto-converted Parquet files:

115 MB

Number of rows:

5,809,104

Models trained or fine-tuned on Genentech/human-chromhmm-fullstack-data

Genentech/human-chromhmm-fullstack-model

Tabular Classification • Updated 2 days ago

Collection including Genentech/human-chromhmm-fullstack-data

gReLU Model Zoo

Collection

Zoo of models and datasets associated with https://github.com/Genentech/gReLU/. Copied from the original zoo on Weights and Biases (https://wandb.ai/) • 17 items • Updated 16 days ago