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21 projects

cyvcf2

Last released

fast vcf parsing with cython + htslib

peddy

Last released

pleasingly pythonic pedigree manipulation

interlap

Last released

interlap: fast, simple interval overlap testing

cpv

Last released

combine p-values

slurmpy

Last released

submit jobs to slurm with python

fisher

Last released

Fast Fisher's Exact Test

quicksect

Last released

fast, simple interval intersection

geneimpacts

Last released

normalize effects from variant annotation tools (snpEff, VEP)

inheritance

Last released

inheritance models for mendelian genetics

toolshed

Last released

Tools for data

cigar

Last released

manipulate SAM cigar strings

skidmarks

Last released

find runs (non-randomness) in sequences

mendelianerror

Last released

probability of mendelian error in trios

bsub

Last released

submit jobs to LSF with python

hts

Last released

cruzdb

Last released

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

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

aclust

Last released

streaming agglomerative clustering

nwalign

Last released

Needleman-Wunsch global sequence alignment

totable

Last released

Cython wrapper for tokyo cabinet table

simpletable

Last released

wrapper around pytables/hd5f to simplify using structured data

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