datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
DNANet_2p5pMixture_PPF6C_2024
2p5p Mixture DNA Research dataset
This dataset repository contains RFU signal reading (.hid) files and their corresponding person mixture labels (.txt) used in the DNANet paper and code.
The data consist of DNA sample mixtures of 2 to 5 persons, of which the mixtures composition is known,
allowing for training on actual ground-truth data for DNA annotation tools such as DNANet
If you use this dataset in your research please cite it appropriately:
@ARTICLE{Benschop2019,
title… See the full description on the dataset page: https://huggingface.co/datasets/NetherlandsForensicInstitute/DNANet_2p5pMixture_PPF6C_2024.ctc-cell-cycle-hela
CTC Cell Cycle Dataset
Cell Tracking Challenge (CTC) live-cell microscopy with derived cell cycle state
labels for 3-class temporal classification.
What's actually hosted
The repo name says hela for historical reasons. Currently hosted: Fluo-N2DH-GOWT1
(GFP-tagged Oct4 in mouse embryonic stem cells), which is what the milestone baseline
trained on. HeLa data may be added later under a hela/ prefix.
Sequence
Frames
Used as
01/
92
training
02/
92
held-out… See the full description on the dataset page: https://huggingface.co/datasets/DnaRnaProteins/ctc-cell-cycle-hela.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.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.genomes-v4-genome_set-animals-intervals-v5_256_128genomes-v4-genome_set-animals-intervals-v4_512_256genomes-v4-genome_set-animals-intervals-v11_256_128genomes-v5-genome_set-animals-intervals-v1_255_128
bolinas-dna/genomes-v5-genome_set-animals-intervals-v1_255_128
Animals promoters (v1) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
8db58254831f). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
68,286,166 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements included). This is… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals-intervals-v1_255_128.genomes-v4-genome_set-animals-intervals-v10_256_128genomes-v4-genome_set-animals-intervals-v12_256_128genomes-v4-genome_set-animals-intervals-v13_256_128genomes-v4-genome_set-animals-intervals-v14_256_128genomes-v4-genome_set-animals-intervals-v7_256_128genomes-v5-genome_set-animals_order204-intervals-v5_255_128
bolinas-dna/genomes-v5-genome_set-animals_order204-intervals-v5_255_128
204 animals (one per order) CDS (v5) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
main). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
101,114,252 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals_order204-intervals-v5_255_128.genomes-v4-genome_set-animals-intervals-v1_256_128picturesgpn-star-p-uniform-v1-cds
marin-dna/gpn-star-p-uniform-v1-cds
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the cds region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses calibrated entropy from the primate… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/gpn-star-p-uniform-v1-cds.genomes-v4-genome_set-animals-intervals-v6_256_128zoonomia-v1-v4_ccre_noexon
bolinas-dna/zoonomia-v1-v4_ccre_noexon
A curated enhancer training set for issue
#326 — a de-contaminated
derivation of the v4 ccre_non_promoter arm of
bolinas-dna/zoonomia-v1-v1,
built by the
snakemake/zoonomia_projection_dataset pipeline at commit
6b320c268547.
Provenance
This subset is the v4 ccre_non_promoter arm with every window that overlaps any other functional element (CDS / 3′UTR / ncRNA exon / TSS+5′UTR) removed — i.e. windows whose functional content… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v4_ccre_noexon.gpn-star-p-uniform-v1-enhancer-arm-a
marin-dna/gpn-star-p-uniform-v1-enhancer-arm-a
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the enhancer region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses calibrated entropy from the primate… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/gpn-star-p-uniform-v1-enhancer-arm-a.gpn-star-p-uniform-v1-background
marin-dna/gpn-star-p-uniform-v1-background
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the background region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses calibrated entropy from the primate… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/gpn-star-p-uniform-v1-background.phylop-uniform-v1-cds
marin-dna/phylop-uniform-v1-cds
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and UCSC hg38 MultiZ 100-way alignment.
This draft covers the cds region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
Anchor eligibility uses the pipeline's pinned phyloP conservation filter.
Sequence… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/phylop-uniform-v1-cds.zoonomia-v1-v4_ccre_noexon_enhancer
bolinas-dna/zoonomia-v1-v4_ccre_noexon_enhancer
A curated enhancer training set for issue
#326 — a de-contaminated
derivation of the v4 ccre_non_promoter arm of
bolinas-dna/zoonomia-v1-v1,
built by the
snakemake/zoonomia_projection_dataset pipeline at commit
6b320c268547.
Provenance
This subset is v4_ccre_noexon further restricted to enhancer-dominant windows (dELS+pELS basepair coverage ≥ the other non-PLS cCRE classes), population-matching the val_enhancer… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v4_ccre_noexon_enhancer.genomes-v4-genome_set-animals-intervals-v8_256_128functional-cds
marin-dna/functional-cds
Human-anchored 255 bp vertebrate sequences from the Zoonomia 447-mammal Cactus alignment and official version-matched UCSC hg38-to-target liftOver chains.
This draft covers the cds region cohort with all species scope and preserves source FASTA/2bit letter case.
Non-human rows project only the central human nucleotide and extract the 255 bp target window centered on its unique mapped locus.
For the 28 non-mammalian targets, the stable ucsc_multiz100way… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/functional-cds.genomes-v5-genome_set-animals-intervals-v5_255_128
bolinas-dna/genomes-v5-genome_set-animals-intervals-v5_255_128
Animals CDS (v5) sequences — 255 bp DNA windows
for genomic language model pretraining.
Part of the bolinas-dna/genomes-v5 training-dataset family produced by the
snakemake/training_dataset pipeline (commit
8db58254831f). Each repo in the family is one
(genome_set, region-recipe) combination.
Size
242,334,716 sequences across 64 data/train/*.jsonl.zst shards
(reverse complements included). This is an… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/genomes-v5-genome_set-animals-intervals-v5_255_128.zoonomia-v1-v3_cds
bolinas-dna/zoonomia-v1-v3_cds
Per-anchor region-type partition of the cross-mammal training set
bolinas-dna/zoonomia-v1-v1,
restricted to anchors labelled cds by the
snakemake/zoonomia_projection_dataset pipeline
(commit 2ab868a2f1d4).
Region label (cds)
Coding sequence — Ensembl r115 CDS features (get_cds). Highest-priority class: any anchor with overlap on a CDS feature (and union-of-functional fraction ≥ 0.20 across all five labels) is labelled cds, regardless… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v3_cds.DNA_Gen
Citation
Please cite our work using the bibtex below:
BibTeX:
@article{su2025language,
title={Language Models for Controllable DNA Sequence Design},
author={Su, Xingyu and Li, Xiner and Lin, Yuchao and Xie, Ziqian and Zhi, Degui and Ji, Shuiwang},
journal={arXiv preprint arXiv:2507.19523},
year={2025}
}
genomes-v4-genome_set-animals-intervals-v9_256_128genomes-v4-genome_set-animals-intervals-v15_256_128