Search Packages

bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

biocommons-seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

tinyhgvs

Hybrid Rust/Python library for parsing HGVS variants.

granite-suite

A collection of software to work with genomic variants

seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

graphmana

Graph-native data management platform for variant genomics

anyvar

Lightweight, portable variation registration and retrieval

variant-extractor

Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.

alphagenome-viewer

Web interface for Google DeepMind's AlphaGenome genomic prediction model

biocommons-anyvar

Lightweight, portable variation registration and retrieval

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

embedpvp

EmbedPVP: Integration of Genomics and Phenotypes for Variant Prioritization using Deep Learning

mrva

A terminal-first approach to CodeQL multi-repo variant analysis

varexpm

A CLI-Tool for extracting context-based process variants from conventional event logs.