cyvcf2

Last released Jun 18, 2024

fast vcf parsing with cython + htslib

fisher

Last released Sep 11, 2023

Fast Fisher's Exact Test

peddy

Last released Jun 2, 2021

pleasingly pythonic pedigree manipulation

interlap

Last released Oct 2, 2020

interlap: fast, simple interval overlap testing

cpv

Last released Sep 29, 2020

combine p-values

slurmpy

Last released Apr 8, 2020

submit jobs to slurm with python

quicksect

Last released Jun 4, 2019

fast, simple interval intersection

geneimpacts

Last released May 22, 2019

normalize effects from variant annotation tools (snpEff, VEP)

inheritance

Last released Jan 16, 2019

inheritance models for mendelian genetics

toolshed

Last released Jun 18, 2016

Tools for data

cigar

Last released Dec 8, 2015

manipulate SAM cigar strings

skidmarks

Last released Sep 16, 2015

find runs (non-randomness) in sequences

mendelianerror

Last released May 26, 2015

probability of mendelian error in trios

bsub

Last released Nov 21, 2014

submit jobs to LSF with python

hts

Last released Jul 18, 2014

cruzdb

Last released Jul 9, 2014

Interface to UCSC genomic databases. Also allows things like up/downstream/k-nearest-neighbor queries and mirroring of tables to local sqlite databases

pyfasta

Last released Apr 3, 2014

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

aclust

Last released Jan 10, 2014

streaming agglomerative clustering

nwalign

Last released Jan 8, 2010

Needleman-Wunsch global sequence alignment

totable

Last released Jan 7, 2010

Cython wrapper for tokyo cabinet table

simpletable

Last released Nov 7, 2009

wrapper around pytables/hd5f to simplify using structured data