brentp

Doing genomics

University of UtahOregon, USA

Pinned Repositories

bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
Language:C182 16 16105
cyvcf2
cython + htslib == fast VCF and BCF processing
Language:Cython412 6 21775
echtvar
using all the bits for echt rapid variant annotation and filtering
Language:Rust152 5 349
goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Language:Go221 16 6825
hts-nim
nim wrapper for htslib for parsing genomics data files
Language:Nim156 9 5627
mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Language:Nim771 21 224100
slivar
genetic variant expressions, annotation, and filtering for great good.
Language:Nim264 9 16525
smoove
structural variant calling and genotyping with existing tools, but, smoothly.
Language:Go257 10 24321
somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Language:Nim290 8 13943
vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Language:Go383 25 14556

brentp's Repositories

brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Language:Nim771 21 224100
brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
Language:Cython412 6 21775
brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
Language:Go383 25 14556
brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Language:Nim290 8 13943
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
Language:Nim264 9 16525
brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
Language:Rust152 5 349
brentp/bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
Language:Python151 12 7858
brentp/peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Language:Jupyter Notebook142 6 8140
brentp/vcfexpress
expressions on VCFs
Language:Rust85 2 14
brentp/vcfgo
a golang library to read, write and manipulate files in the variant call format.
Language:Go71 7 1320
brentp/fishers_exact_test
Fishers Exact Test for Python (Cython)
Language:Python66 4 3323
brentp/geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
Language:Python34 3 916
brentp/fraguracy
overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites
Language:Rust33 2 113
brentp/nim-lapper
fast easy interval overlapping for nim-lang
Language:Nim28 4 24
brentp/pbr
drunk on perbase pileups and lua expressions
Language:Rust19 2 82
brentp/bix
tabix file access with golang using biogo machinery
Language:Go10 4 115
brentp/xvcf-rs
VCF/BCF [un]compressed [un]indexed
Language:Rust9 2 0
brentp/bedder-rs
an API for intersections of genomic data
Language:Rust5 4 10
brentp/d4-nim
nim-lang wrapper for https://github.com/38/d4-format
Language:Nim5 1 01
brentp/bedder-py-wrappers
rust->python wrappers to be used by bedder
Language:Rust4
brentp/simplebed-rs
a simple bed file reader and writer that allows querying when an index is present
Language:Rust41
brentp/fgoxide
Quality of life improvements in Rust.
Language:Rust1 1 0
brentp/noodles
Bioinformatics I/O libraries in Rust
Language:Rust1 0 0
brentp/perbase
Per-base per-nucleotide depth analysis
Language:Rust1 1 0
brentp/bedder-docs
documentation for bedder in mkdocs
Language:Python1
brentp/help-repositories
getting help on stuff.
Language:Rust2 0
brentp/hts-sys
Raw rust bindings for htslib
brentp/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:Rust0 0
brentp/rust-htslib
This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
Language:Rust1 0
brentp/vembrane-benchmark
benchmark workflow for vcfexpress paper
Language:Python