Genome Python Packages

pyfastx

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

pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

pyrodigal

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

genomepy

genes and genomes at your fingertips

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.

pyaragorn

Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.

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/

genet

Python library for genome editing, CRISPR gRNA design and prediction

pyani-plus

Development repo for pyani-plus (the next iteration of pyani)

doublehelix

Genomic data manipulation tool

jbrowse-jupyter

A python package for showing JBrowse views

codonu

An integrated package for codon usage analysis

corda

Genome-scale model construction with CORDA

coretracker

CoreTracker, A codon reassignment tracker

arv

A fast 23andMe DNA parser and inferrer for Python

variant-spark

machine learning for genomic variants

perf-ssr

PERF is an exhaustive repeat finder

amplicov

interactive barplot for amplicon sequencing

dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

metaomestats

Statistical package for metaome denovo assembly results.

mutation-simulator

A tool for simulating random mutations in any genome

vcfsynonymous

read VCF and select synonymous or non-synonymous coding variants

gcnframe

This is a python package for genomics study with a GCN framework.