Brent Pedersen (brentp)

brentp

User data from Github https://github.com/brentp

Company:University of Utah

Location:Oregon, USA

GitHub:@brentp

Twitter:@brent_p


Organizations
quinlan-lab

Brent Pedersen's repositories

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language:NimLicense:MITStargazers:729Issues:21Issues:219

cyvcf2

cython + htslib == fast VCF and BCF processing

Language:CythonLicense:MITStargazers:392Issues:6Issues:217

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

Language:GoLicense:MITStargazers:371Issues:25Issues:144

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

Language:NimLicense:MITStargazers:276Issues:8Issues:134

slivar

genetic variant expressions, annotation, and filtering for great good.

Language:NimLicense:MITStargazers:255Issues:9Issues:163

smoove

structural variant calling and genotyping with existing tools, but, smoothly.

Language:GoLicense:Apache-2.0Stargazers:248Issues:11Issues:243

goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Language:GoLicense:MITStargazers:219Issues:17Issues:68

hts-nim

nim wrapper for htslib for parsing genomics data files

Language:NimLicense:MITStargazers:155Issues:9Issues:56

echtvar

using all the bits for echt rapid variant annotation and filtering

Language:RustLicense:MITStargazers:148Issues:5Issues:31

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

Language:PythonLicense:MITStargazers:147Issues:12Issues:78

vcfexpress

expressions on VCFs

Language:RustLicense:MITStargazers:78Issues:2Issues:0

vcfgo

a golang library to read, write and manipulate files in the variant call format.

Language:GoLicense:MITStargazers:69Issues:8Issues:13

fishers_exact_test

Fishers Exact Test for Python (Cython)

Language:PythonLicense:BSD-3-ClauseStargazers:64Issues:4Issues:33

rare-disease-wf

(WIP) best-practices workflow for rare disease

Language:NextflowLicense:MITStargazers:60Issues:8Issues:10

fraguracy

overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites

Language:RustLicense:MITStargazers:33Issues:2Issues:11

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

Language:PythonLicense:MITStargazers:33Issues:4Issues:9

xvcf-rs

VCF/BCF [un]compressed [un]indexed

Language:RustLicense:MITStargazers:9Issues:2Issues:0

go-blosc

go wrapper for blosc (blocked number compression with fast random access)

Language:GoLicense:MITStargazers:5Issues:4Issues:0

bedder-py-wrappers

rust->python wrappers to be used by bedder

Language:RustLicense:MITStargazers:4Issues:0Issues:0

d4-nim

nim-lang wrapper for https://github.com/38/d4-format

Language:NimLicense:MITStargazers:4Issues:1Issues:0

simplebed-rs

a simple bed file reader and writer that allows querying when an index is present

Language:RustLicense:MITStargazers:4Issues:0Issues:0

svtyper

Bayesian genotyper for structural variants

Language:PythonLicense:MITStargazers:3Issues:5Issues:0
Language:NextflowStargazers:2Issues:0Issues:0

fgoxide

Quality of life improvements in Rust.

Language:RustLicense:MITStargazers:1Issues:1Issues:0

noodles

Bioinformatics I/O libraries in Rust

License:MITStargazers:1Issues:0Issues:0

help-repositories

getting help on stuff.

Language:RustLicense:MITStargazers:0Issues:2Issues:0

hts-sys

Raw rust bindings for htslib

License:MITStargazers:0Issues:0Issues:0

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Language:RustLicense:MITStargazers:0Issues:0Issues:0

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

Language:RustLicense:MITStargazers:0Issues:1Issues:0

vembrane-benchmark

benchmark workflow for vcfexpress paper

Language:PythonLicense:MITStargazers:0Issues:0Issues:0