GPN
Datasets
All datasets matching “GPN”gpn-star-scores
GPN-Star genome-wide scores
Genome-wide, mutation-rate-calibrated GPN-Star constraint and variant scores for
eight score sets covering human, mouse, chicken, D. melanogaster,
C. elegans, and A. thaliana. Canonical scores are available as
chromosome-sharded Parquet. Hugging Face hosts 72 BigWigs; a multi-assembly
UCSC track hub references the 64 logo/LLR views.
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Default Dataset… See the full description on the dataset page: https://huggingface.co/datasets/songlab/gpn-star-scores.gpn-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.gpn-animal-promoter-datasetgpn-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-msa-hg38-scores
GPN-MSA predictions for all possible SNPs in the human genome (~9 billion)
For more information check out our paper and repository.
Querying specific variants or genes
Install the latest tabix:In your current conda environment (might be slow):conda install -c bioconda -c conda-forge htslib=1.18
or in a new conda environment:conda create -n tabix -c bioconda -c conda-forge htslib=1.18
conda activate tabix
Query a specific region (e.g. BRCA1), from the remote file:… See the full description on the dataset page: https://huggingface.co/datasets/songlab/gpn-msa-hg38-scores.gpn_grass