datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
dna_rendering_processed
DNA-Rendering-Processed Dataset
Project Page | Paper | Code | Model
To enable Diffuman4D model training, we meticulously process the DNA-Rendering dataset by recalibrating camera parameters, optimizing image color correction matrices (CCMs), predicting foreground masks, and estimating human skeletons.
To promote future research in the field of human-centric 3D/4D generation, we have open-sourced our re-annotated labels for the DNA-Rendering dataset in this repo, which includes… See the full description on the dataset page: https://huggingface.co/datasets/krahets/dna_rendering_processed.annotators
Genomic Variant Annotators
Curated genomic variant annotation modules from the DNA-seq project.
Overview
This dataset contains pre-computed annotation data for genetic variants, organized by module:
Module
Description
Files
longevitymap
Longevity-associated variants
annotations.parquet, studies.parquet, weights.parquet
Schema
annotations.parquet
Variant-level facts linking rsIDs to genes and phenotypes.
rsid: dbSNP… See the full description on the dataset page: https://huggingface.co/datasets/just-dna-seq/annotators.human_ref_dna
Dataset Card for "human_ref_dna"
More Information needed
clinvarbacbench-phenotypic-traits-dna
Dataset for phenotypic traits prediction from whole bacterial genomes (DNA)
A dataset of 24,462 bacterial genomes across 15,477 species with diverse phenotypic traits as labels.
The genome protein sequences have been extracted from GenBank. Each row contains the whole bacterial genome DNA, with the DNA from different contigs separated by a space.
The phenotypic traits have been extracted from a number of sources [1, 2, 3] and include a diversity of categorical phenotypes. We exclude… See the full description on the dataset page: https://huggingface.co/datasets/macwiatrak/bacbench-phenotypic-traits-dna.alphagenome_avi
AlphaGenome AVI scores, re-encoded
AlphaGenome's Variant Impact (AVI) scores for 8,812,917,339 SNVs on GRCh38, re-encoded from
the 88.5 GB published tabix TSV into ~34 GB of parquet by
just-dna-enricher.
This is a re-encoding, not a re-analysis. No score is changed, recomputed or filtered.
What is in it
data/alphagenome_avi-<contig>.parquet
chrom, pos (1-based VCF), ref, alt, raw_score_e5
avi_knots.parquet
the PHRED reconstruction curve — not… See the full description on the dataset page: https://huggingface.co/datasets/just-dna-seq/alphagenome_avi.prs-percentilesHuman_DNA_v0_DNABert6tokenized_stride1rag-five-regions-v1-utr3
marin-dna/rag-five-regions-v1-utr3
Human-anchored RAG documents for the utr3 region.
The producing workflow owns source identities, projected coordinates, and sequence provenance at s3://oa-bolinas/snakemake/vertebrate_projection_dataset/results/rag-five-regions-v1/6b1593c274a886d20f5c0ddf3712916d446f5fed/10ba63bc375ba912909b82cda68143df4677431124fc8e15f6ac42850ce0fca6/full/rag.
The publishing workflow owns public shard row mappings and release checksums at… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/rag-five-regions-v1-utr3.Human_DNA_v0_Perceiver1tokenizedHuman_DNA_v0_K8tokenized_stride1ec_classification_dnalaya-bio
Laya-Bio: short-sequence candidate-scoring benchmark and reproducibility data
This repository packages the data and saved results used by Laya-Bio: Candidate Scoring and Reliability on Short Biological Sequences (Liang Wang, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology). The main study uses two closed-set tasks, four model conditions and three training seeds, with no additional neural continual pretraining.
Companion… See the full description on the dataset page: https://huggingface.co/datasets/dnagpt/laya-bio.ensembl_variations
Ensembl Variations (Parquet Format)
This dataset contains Ensembl human genetic variations converted to Parquet format for fast and efficient VCF annotation.
Usage
With Polars (Recommended)
import polars as pl
# Load variants for chromosome 21
df = pl.scan_parquet("hf://datasets/just-dna-seq/ensembl_variations/data/homo_sapiens-chr21.parquet")
# Filter variants by position
variants = df.filter(
(pl.col("POS") >= 10000000) & (pl.col("POS") <= 20000000)… See the full description on the dataset page: https://huggingface.co/datasets/just-dna-seq/ensembl_variations.virus_dna_dataset[Needs More Information]
Dataset Card for virus_dna_dataset
Dataset Summary
A collection of full virus genome dna, the dataset was built from NCBI data
Supported Tasks and Leaderboards
[Needs More Information]
Languages
DNA
Dataset Structure
Data Instances
{ 'Description' : 'NC_030848.1 Haloarcula californiae icosahedral...', 'dna_sequence' : 'TCATCTC TCTCTCT CTCTCTT GTTCCCG CGCCCGC CCGCCC...',
'sequence_length':'35787'… See the full description on the dataset page: https://huggingface.co/datasets/Hack90/virus_dna_dataset.Zebrafish_DNA_v0_tokenized_kmer6_stride1rag-five-regions-v1-cds
marin-dna/rag-five-regions-v1-cds
Human-anchored RAG documents for the cds region.
The producing workflow owns source identities, projected coordinates, and sequence provenance at s3://oa-bolinas/snakemake/vertebrate_projection_dataset/results/rag-five-regions-v1/6b1593c274a886d20f5c0ddf3712916d446f5fed/10ba63bc375ba912909b82cda68143df4677431124fc8e15f6ac42850ce0fca6/full/rag.
The publishing workflow owns public shard row mappings and release checksums at… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/rag-five-regions-v1-cds.zoonomia-rag-v1-v1
bolinas-dna/zoonomia-rag-v1-v1
Fixed-layout 2,048-token documents built from conservation-filtered GRCh38
255-base anchors, seven fixed Zoonomia mammalian ortholog slots, and a final
human slot. Missing non-human projections are filled with 255 N bases;
chromosome 18 is validation-only.
Produced by the commit-pinned issue #402 RAG pipeline. The
immutable upstream input is the existing Zoonomia v1
min0.20/all_species_with_sequence.parquet projection. No halLiftover was
run for… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-rag-v1-v1.Human_DNA_v0_K7tokenized_stride1bacbench-antibiotic-resistance-dna
Dataset for antibiotic resistance prediction from whole-bacterial genomes (DNA)
A dataset of 25,032 bacterial genomes across 39 species with antimicrobial resistance labels.
The genome DNA sequences have been extracted from GenBank. Each row contains whole bacterial genome, with spaces
separating different contigs present in the genome.
The antimicrobial resistance labels have been extracted from Antibiotic Susceptibility Test (AST) Browser, accessed 23 Oct, 2024.)
and include both… See the full description on the dataset page: https://huggingface.co/datasets/macwiatrak/bacbench-antibiotic-resistance-dna.rag-five-regions-v1-ncrna
marin-dna/rag-five-regions-v1-ncrna
Human-anchored RAG documents for the ncrna region.
The producing workflow owns source identities, projected coordinates, and sequence provenance at s3://oa-bolinas/snakemake/vertebrate_projection_dataset/results/rag-five-regions-v1/6b1593c274a886d20f5c0ddf3712916d446f5fed/10ba63bc375ba912909b82cda68143df4677431124fc8e15f6ac42850ce0fca6/full/rag.
The publishing workflow owns public shard row mappings and release checksums at… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/rag-five-regions-v1-ncrna.evals_mendelian_traits
evals_mendelian_traits
Variant-effect-prediction benchmark of pathogenic Mendelian SNVs vs gnomAD
common SNVs, 1:9 matched within consequence categories on (chrom, consequence_final) plus subset-targeted distance bins.
Description
Positives
OMIM ∪ Smedley et al. 2016 ∪ HGMD (latter via Sei, Chen et al. Nat Genet 2022), deduplicated, gnomAD AF<0.001
Negatives
gnomAD common: AN≥25 000 and AF>0.001, 1:9 matched per positive
Genome build
GRCh38… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/evals_mendelian_traits.pgs-catalog
PGS Catalog — Scoring Files & Cleaned Metadata
Complete mirror of PGS Catalog scoring files converted to
Apache Parquet format, together with cleaned and normalised metadata tables.
Built automatically by the just-prs pipeline.
Last updated: 2026-06-14 16:02 UTC
Release Statistics
Metric
Value
Scoring file parquets
5,337
Unique PGS IDs (metadata)
5,337
Genome build
GRCh38
Total scoring data size
52.6 GB
Release timestamp
2026-06-14T16:02:29Z… See the full description on the dataset page: https://huggingface.co/datasets/just-dna-seq/pgs-catalog.DNA_coding_regions
DNA Coding Regions Dataset
This is a curated collection of genomic sequences extracted directly from NCBI GenBank, designed to support research in introns and exons classification, DNA-to-protein translation, gene structure analysis, and biological sequence modeling with deep learning architectures.
Source and Extraction Pipeline
All records were extracted from GenBank using Biopython.The dataset construction followed a reproducible data processing pipeline written in… See the full description on the dataset page: https://huggingface.co/datasets/shefat16/DNA_coding_regions.rag-five-regions-v1-enhancer
marin-dna/rag-five-regions-v1-enhancer
Human-anchored RAG documents for the enhancer region.
The producing workflow owns source identities, projected coordinates, and sequence provenance at s3://oa-bolinas/snakemake/vertebrate_projection_dataset/results/rag-five-regions-v1/6b1593c274a886d20f5c0ddf3712916d446f5fed/10ba63bc375ba912909b82cda68143df4677431124fc8e15f6ac42850ce0fca6/full/rag.
The publishing workflow owns public shard row mappings and release checksums at… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/rag-five-regions-v1-enhancer.Human_DNA_v0bacbench-filtered-dnaaligned_seqshuman_genome_GCF_009914755.1
Dataset Card for "human_genome_GCF_009914755.1"
how to build this data:
human full genome data from:
https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009914755.1/
Preprocess:
1 download data use ncbi data set tools:
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets'
chmod +x datasets
./datasets download genome accession GCF_000001405.40 --filename genomes/human_genome_dataset.zip
then move the gene data to human2.fra
2 write the… See the full description on the dataset page: https://huggingface.co/datasets/dnagpt/human_genome_GCF_009914755.1.DNA_coding_regions
DNA Coding Regions Dataset
This is a curated collection of genomic sequences extracted directly from NCBI GenBank, designed to support research in introns and exons classification, DNA-to-protein translation, gene structure analysis, and biological sequence modeling with deep learning architectures.
Source and Extraction Pipeline
All records were extracted from GenBank using Biopython.The dataset construction followed a reproducible data processing pipeline written in… See the full description on the dataset page: https://huggingface.co/datasets/GustavoHCruz/DNA_coding_regions.