brentp

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University of Utah

Utrecht, The Netherlands

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quinlan-lab

Brent Pedersen's repositories

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

Language:CMIT181 16 16

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.

Language:PythonMIT101 6 8

quicksect

a cythonized, extended version of the interval search tree in bx

Language:PythonMIT30 5 11

toolshed

python stuff I use

Language:PythonBSD-2-Clause19 5 1

bix

tabix file access with golang using biogo machinery

Language:GoMIT9 4 1

bamject

DO NOT USE inject variants (snps/indels) from a vcf into a bam efficiently.

Language:NimMIT7 3 1

falas

Fragment-Aware Local Assembly for Short-reads

Language:NimMIT7 30

inheritance

inheritance models for mendelian diseases

Language:PythonMIT7 3 2

bpbio

basepair bio: a single binary with many useful genomics subtools.

Language:NimMIT6 3 5

variantkey-nim

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

Language:CMIT4 3 1

ksw2-nim

nim wrapper for lhs/ksw2 for fast smith-waterman

Language:CMIT3 30

nim-cgranges

nim wrapper for https://github.com/lh3/cgranges for faster interval tree

Language:CMIT3 30

nimpress

Polygenic score calculation from VCF in Nim.

Language:NimMIT3 20

svtyper

Bayesian genotyper for structural variants

Language:PythonMIT2 30

brentp.github.io

blog hosting

Language:HTML1 40

GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Language:C++Apache-2.01 20

samplot

Plot structural variant signals from many BAMs and CRAMs

Language:Python1 30

svtools

Tools for processing and analyzing structural variants.

Language:PythonMIT1 20

Arraymancer

A fast, ergonomic and portable tensor library in Nim with a deep learning focus for CPU, GPU and embedded devices via OpenMP, Cuda and OpenCL backends

Language:NimApache-2.0020

conda

OS-agnostic, system-level binary package manager and ecosystem

Language:PythonNOASSERTION030

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language:PythonBSD-3-Clause020

docopt.nim

Command line arguments parser that will make you smile (port of docopt to Nim)

Language:NimMIT030

duktape-nim

Nim wrapper for the Duktape embeddable Javascript engine.

Language:C030

hugo-blog

not rendered content. ignore.

Language:HTMLMIT030

libBigWig

A C library for handling bigWig files

Language:CMIT020

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Language:PythonGPL-3.0020

NAHRly

Genomic copy-number variant calling on NAHR-based events

Language:Python030

nlvm

LLVM-based compiler for the Nim language

Language:NimNOASSERTION020

packages

List of packages for Nimble

Language:Nim030

zip

Wrapper for the zip library

Language:CMIT030