Search Packages

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

genomepy

genes and genomes at your fingertips

pyaragorn

Cython bindings and Python interface to ARAGORN, a tRNA and mtRNA detection software.

intronic

Retrieve annotated intron sequences from an annotated genome and classify them as minor (U12-type) or major (U2-type) using a support vector machine model.

edge-genome

Efficiently keep track of changes to genomes

wormneuroatlas

Neural signal propagation atlas (Randi et al.), genome (WormBase), single-cell transcriptome (Taylor et al.), neuropeptide/GPCR deorphanization (Beets et al.), monoaminergic connectome (Bentley et al.), and chemical-synapse sign predictions (Fenyves et al.) all in one place. Read the docs: https://francescorandi.github.io/wormneuroatlas/

variant-spark

machine learning for genomic variants

genet

GenET: Genome Editing Toolkit

jbrowse-jupyter

A python package for showing JBrowse views

py-crispr-analyser

Python module and scripts to analyse CRISPRs and off-targets from a genome

pyani-plus

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

corda

Genome-scale model construction with CORDA

doublehelix

Genomic data manipulation tool

coretracker

CoreTracker, a codon reassignment tracker

codonu

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

arv

A fast 23andMe raw genome file parser

vcfsynonymous

read VCF and select synonymous or non-synonymous coding variants

amplicov

script to generate amplicon coverage plot

dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

genhub

Explore eukaryotic genome composition and organization with iLoci

mutation-simulator

A tool for simulating random mutations in any genome

metaomestats

Statistical package for metaome denovo assembly results.