Genome Python Packages

pyrodigal

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

52K 188 11

pyfastx

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

47K 296 25

pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

46K 107 15

genomepy

genes and genomes at your fingertips

30K 410 41

coralsnake

Exon-aware RNA pipeline: splicing-aware liftover (tbam2gbam/gbam2tbam), metagene, annotation

16K 0 1

magenpy

Modeling and Analysis of (Statistical) Genetics data in python

5K 22 5

pyaragorn

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

2K 10 1

genome-spy-python

genome-spy-python is a declarative genomics visualization library for Python, built on top of the genome-spy JSON specification.

2K 26 1

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/

1K 11 8

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.

1K 9 1