enhancer
Datasets
All datasets matching “enhancer”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.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.functional-enhancer
marin-dna/functional-enhancer
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 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.
For the 28 non-mammalian targets, the stable… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/functional-enhancer.phylop-uniform-v1-enhancer-arm-a
marin-dna/phylop-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 the pipeline's pinned phyloP conservation… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/phylop-uniform-v1-enhancer-arm-a.DeepSTARR-enhancer-activity
Abouts
The enhancer activity data is sourced from the DeepSTARR repo.
We have applied minor formatting adjustments to the dataset to facilitate streamlined data analysis.
How to use
from datasets import load_dataset
datasets = load_dataset("GenerTeam/DeepSTARR-enhancer-activity")
vertebrate-v1-issue473-fullwindow-ccre-enhancer-centered
marin-dna/vertebrate-v1-issue473-fullwindow-ccre-enhancer-centered
Review status: draft generated for issue #473 review before upload.
Human-anchored 255 bp vertebrate sequences for the
ccre_enhancer_centered cohort under the full_window policy.
The policy projects the complete 255 bp human window, applies the established 128--512 bp compatible-fragment gate, and resizes around the accepted target-span midpoint. Human anchors come from the fixed exp351 ENCODE dELS/pELS-centered… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/vertebrate-v1-issue473-fullwindow-ccre-enhancer-centered.