Genome Python Packages

pyfastx

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

88K 294 24

pyrodigal

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

77K 184 10

pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

60K 101 15

genomepy

genes and genomes at your fingertips

21K 412 41

pyaragorn

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

2K 10 1

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.

2K 9 1

edge-genome

Efficiently keep track of changes to genomes

2K 38 4

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/

2K 7 8