hvantk

Onboard, build, or update the ClinGen Gene-Disease Validity resource for hvantk

Onboard, build, or update the ClinVar resource for hvantk

Build a Hail Table from GTEx cis-eQTL summary statistics (per-tissue significant variant-gene pairs) for qtlcascade and variant annotation.

Build a Hail Table from the EBI GWAS Catalog v1.0 full-associations TSV for variant-annotation joins.

Build a Hail Table from the Interactome Insider genomic BED (protein-protein interface residues projected to GRCh38) for interval-based variant annotation.

Build a Hail Table from an MSigDB GMT gene-set file (e.g., C2 Canonical Pathways) for enrichment / burden / overlap analyses.

HGNC gene nomenclature lookup table — authoritative human gene symbols, IDs, and cross-references keyed by hgnc_id.

Build an AnnData object from an EBI Expression Atlas baseline bulk-RNA-seq experiment (TPM expression matrix + SDRF sample metadata).

Onboard, build, or update a UCSC Cell Browser single-cell expression resource for hvantk

Onboard, build, or update the GenCC submissions resource for hvantk

Download and parse a PeptideAtlas Human Phospho build into a wide intermediate TSV consumed by the hvantk PTM pipeline.

Conventions every hvantk plugin assumes. Read first.

Build an AnnData (samples x genes) from long-format CPTAC protein-expression matrices plus sample metadata.

Download CPTAC phosphoproteomics data via the cptac Python package and build a sites x samples AnnData plus a wide intermediate TSV for the hvantk PTM pipeline.

Onboard, build, or update the UniProt PTM sites resource for hvantk