Brent Pedersen (brentp)

brentp

Geek Repo

Company:University of Utrecht

Location:Utrecht, Netherlands

Twitter:@brent_p

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quinlan-lab
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Brent Pedersen's repositories

mosdepth

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

Language:NimLicense:MITStargazers:484Issues:18Issues:155

cyvcf2

cython + htslib == fast VCF and BCF processing

Language:CythonLicense:MITStargazers:302Issues:8Issues:175

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

Language:GoLicense:MITStargazers:299Issues:24Issues:134

smoove

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

Language:GoLicense:Apache-2.0Stargazers:174Issues:10Issues:189

slivar

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

Language:NimLicense:MITStargazers:168Issues:9Issues:122

somalier

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

Language:NimLicense:MITStargazers:168Issues:10Issues:91

hts-nim

nim wrapper for htslib for parsing genomics data files

Language:NimLicense:MITStargazers:146Issues:9Issues:52

bwa-meth

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

Language:PostScriptLicense:MITStargazers:96Issues:12Issues:64

jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Language:NimLicense:MITStargazers:95Issues:3Issues:18

echtvar

echt rapid variant annotation and filtering

Language:RustLicense:MITStargazers:82Issues:1Issues:18

xopen

open files for buffered reading and writing in #golang

Language:GoLicense:MITStargazers:58Issues:4Issues:2

fishers_exact_test

Fishers Exact Test for Python (Cython)

Language:PythonLicense:BSD-3-ClauseStargazers:55Issues:4Issues:28

rare-disease-wf

(WIP) best-practices workflow for rare disease

Language:NextflowLicense:MITStargazers:48Issues:6Issues:10

bsub

python wrapper to submit jobs to bsub (and later qsub)

combined-pvalues

combining p-values using modified stouffer-liptak for spatially correlated results (probes)

Language:PythonLicense:MITStargazers:37Issues:3Issues:31

geneimpacts

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

Language:PythonLicense:MITStargazers:28Issues:3Issues:6

tiwih

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.

Language:NimLicense:MITStargazers:26Issues:2Issues:0

nim-lapper

fast easy interval overlapping for nim-lang

Language:NimLicense:MITStargazers:24Issues:3Issues:2

nim-kmer

DNA kmer operations for nim

Language:NimLicense:MITStargazers:15Issues:2Issues:2

tnsv

add true-negative SVs from a population callset to a truth-set.

Language:NimLicense:MITStargazers:15Issues:2Issues:0

vcf-bench

evaluating vcf parsing libraries

Language:ZigLicense:MITStargazers:14Issues:2Issues:0

hts-zig

ziglang + htslib

Language:ZigLicense:MITStargazers:10Issues:2Issues:0

d4-nim

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

Language:NimLicense:MITStargazers:3Issues:0Issues:0

nim-minizip

nothing to see here.

Language:CStargazers:2Issues:2Issues:0

alignment-nf

Whole Exome/Whole Genome Sequencing alignment pipeline

Language:NextflowLicense:GPL-3.0Stargazers:0Issues:1Issues:0

libvbyte

A fast implementation for varbyte 32bit/64bit integer compression

Language:CLicense:Apache-2.0Stargazers:0Issues:0Issues:0

nibsv

SV genotyping with kmers (created during Baylor hackathon)

Language:NimLicense:MITStargazers:0Issues:0Issues:0
Language:PythonStargazers:0Issues:2Issues:0

sv-channels

Deep learning-based structural variant caller

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:0Issues:1Issues:0

vbyte-zig

vbyte compression for zig using https://github.com/cruppstahl/libvbyte

Language:ZigLicense:MITStargazers:0Issues:0Issues:0