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/).

dajin2

🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing

cpg-workflows

CPG workflows for Hail Batch

nolzss

Non-overlapping Lempel–Ziv–Storer–Szymanski Factorization Python Library

plastburstalign

A Python tool to extract and align genes, introns, and intergenic spacers across thousands of plastid genomes using associative arrays

seqrepo

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

gramep

GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle

helen

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

pyani-plus

pyANI-plus is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity and similar methods.

doublehelix

Genomic data manipulation tool

nanorepeat

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

codonu

A python project for analysis of codon usage for gene or genome analysis

intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

anyvar

Lightweight, portable variation registration and retrieval

biocommons-anyvar

Lightweight, portable variation registration and retrieval

genomehouse

Modular bioinformatics toolkit for sequence analysis, genomic data parsing, machine learning, and visualization all in one package.

seqrepo-rest-service

OpenAPI-based REST interface to biological sequences and sequence metadata

maxatac

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

wigman

Generate heatmap plots from genomic BigWig data

makegms

Genome mappability estimation tool