zoonomia
Datasets
All datasets matching “zoonomia”zoonomia-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.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.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.zoonomia-v1-v3_ccre_non_promoter
bolinas-dna/zoonomia-v1-v3_ccre_non_promoter
Per-anchor region-type partition of the cross-mammal training set
bolinas-dna/zoonomia-v1-v1,
restricted to anchors labelled ccre_non_promoter by the
snakemake/zoonomia_projection_dataset pipeline
(commit 2ab868a2f1d4).
Region label (ccre_non_promoter)
ENCODE cCRE V4 non-promoter classes — cre_class != "PLS" (so: dELS, pELS, CA, CA-CTCF, CA-TF, CA-H3K4me3, TF), extended by 500 bp on each side. PLS is excluded because… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v3_ccre_non_promoter.zoonomia-v1-v1
zoonomia-v1-v1
255 bp human-anchored windows, conservation-filtered (phyloP_447m, proportion_conserved >= 0.20), projected onto 108 family-deduped Zoonomia 447-mammalian assemblies via halLiftover, midpoint-resized to 255 bp, reverse-complement-augmented. Single train split.
Produced by the zoonomia_projection_dataset pipeline in Open-Athena/bolinas-dna — permalinked at the exact code that built this dataset: snakemake/zoonomia_projection_dataset @ 7ff07cd (PR #158).… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v1.zoonomia-v1-v3_ncrna_exon
bolinas-dna/zoonomia-v1-v3_ncrna_exon
Per-anchor region-type partition of the cross-mammal training set
bolinas-dna/zoonomia-v1-v1,
restricted to anchors labelled ncrna_exon by the
snakemake/zoonomia_projection_dataset pipeline
(commit 2ab868a2f1d4).
Region label (ncrna_exon)
Non-coding-RNA exon — every Ensembl r115 exon that is not part of a protein-coding transcript (get_exons(ann) − get_ensembl_protein_coding_exons(ann)). No biotype or quality filter, so this… See the full description on the dataset page: https://huggingface.co/datasets/marin-dna/zoonomia-v1-v3_ncrna_exon.