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Alan Rubin's Projects

biocommons.seqrepo icon biocommons.seqrepo

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

bioutils icon bioutils

bioutils provides some common tools and lookup tables used primarly by the hgvs and uta packages

fqread icon fqread

Python library for FASTQ file handling.

gitignore icon gitignore

A collection of useful .gitignore templates

hgvs icon hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

idutils icon idutils

Small Python library to validate persistent identifiers used in scholarly communication.

mave_ga4gh icon mave_ga4gh

linkml representation of MAVE controlled vocabulary terms

metapub icon metapub

Python toolkit for NCBI metadata (via eutils) and pubmed article text mining -- official primary repo.

pacrat icon pacrat

Improving long-read barcode-variant mapping using multiple sequence alignment.

regolith-i3 icon regolith-i3

An unofficial fork of an unofficial fork (i3-gaps) of i3-wm.

uta icon uta

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

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