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  brentp

23 projects

cyvcf2

Last released on Jul 19, 2018

fast vcf parsing with cython + htslib

quicksect

Last released on Jul 19, 2018

fast, simple interval intersection

peddy

Last released on May 30, 2018

pleasingly pythonic pedigree manipulation

geneimpacts

Last released on Apr 30, 2018

normalize effects from variant annotation tools (snpEff, VEP)

cpv

Last released on Feb 21, 2018

combine p-values

interlap

Last released on Sep 6, 2017

interlap: fast, simple interval overlap testing

fisher

Last released on Aug 30, 2017

Fast Fisher's Exact Test

slurmpy

Last released on Feb 22, 2017

submit jobs to slurm with python

inheritance

Last released on Oct 1, 2016

inheritance models for mendelian genetics

ggd

Last released on Aug 29, 2016

CLI for gogetdata (ggd)

toolshed

Last released on Jun 18, 2016

Tools for data

pedagree

Last released on Apr 6, 2016

pleasingly pythonic pedigree manipulation

cigar

Last released on Dec 8, 2015

manipulate SAM cigar strings

skidmarks

Last released on Sep 16, 2015

find runs (non-randomness) in sequences

mendelianerror

Last released on May 26, 2015

probability of mendelian error in trios

bsub

Last released on Nov 21, 2014

submit jobs to LSF with python

hts

Last released on Jul 18, 2014

cruzdb

Last released on 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 on Apr 3, 2014

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

aclust

Last released on Jan 10, 2014

streaming agglomerative clustering

nwalign

Last released on Jan 8, 2010

Needleman-Wunsch global sequence alignment

totable

Last released on Jan 7, 2010

Cython wrapper for tokyo cabinet table

simpletable

Last released on Nov 7, 2009

wrapper around pytables/hd5f to simplify using structured data

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