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Genome Python Packages

Python packages with the GitHub topic genome. Sorted by relevance, with stars and monthly downloads.
lmdu
pyfastx

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

88K 294 24
althonos
pyrodigal

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

77K 184 10
konstantint
pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

60K 101 15
vanheeringen-lab
genomepy

genes and genomes at your fingertips

21K 412 41
althonos
pyaragorn

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

2K 10 1
glarue
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
ginkgobioworks
edge-genome

Efficiently keep track of changes to genomes

2K 38 4
francescorandi
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
aehrc
variant-spark

machine learning for genomic variants

1K 147 48
Goosang-Yu
genet

GenET: Genome Editing Toolkit

1K 21 6
GMOD
jbrowse-jupyter

A python package for showing JBrowse views

1K 27 4
sanger-cellular-informatics
py-crispr-analyser

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

742 0 0
pyani-plus
pyani-plus

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

685 32 2
DoubleHelixApp
doublehelix

Genomic data manipulation tool

587 6 0
cdiener
corda

Genome-scale model construction with CORDA

527 25 8
SouradiptoC
codonu

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

515 25 1
UdeM-LBIT
coretracker

CoreTracker, a codon reassignment tracker

506 6 3
cslarsen
arv

A fast 23andMe raw genome file parser

479 123 7
rkmlab
perf-ssr

PERF is an exhaustive repeat finder

428 33 11
Grelot
vcfsynonymous

read VCF and select synonymous or non-synonymous coding variants

414 1 0
chienchi
amplicov

script to generate amplicon coverage plot

406 13 5
genotoul-bioinfo
dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

401 113 13
standage
genhub

Explore eukaryotic genome composition and organization with iLoci

335 6 3
raw-lab
metaomestats

Statistical package for metaome denovo assembly results.

314 2 33
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