Projects in Awesome Lists by brentp
A curated list of projects in awesome lists by brentp .
https://github.com/brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
coverage depth exome genome hacktoberfest nim nim-lang sequencing wgs
Last synced: 11 Mar 2025
https://github.com/brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
annotation bioinformatics genomics vcf
Last synced: 12 Apr 2025
https://github.com/brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
bioinformatics cython genomics htslib vcf
Last synced: 11 Mar 2025
https://github.com/brentp/somalier
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
bioinformatics cancer-genomics genomics
Last synced: 11 Mar 2025
https://github.com/brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
genomics rare-disease rare-variant-analysis variant-analysis variant-interpretation
Last synced: 11 Mar 2025
https://github.com/brentp/smoove
structural variant calling and genotyping with existing tools, but, smoothly.
genomics lumpy structural-variation
Last synced: 04 Apr 2025
https://github.com/brentp/goleft
goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
bioinformatics coverage depth genomics golang
Last synced: 09 Apr 2025
https://github.com/brentp/bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
Last synced: 03 Apr 2025
https://github.com/brentp/hts-nim
nim wrapper for htslib for parsing genomics data files
bioinformatics genomics high-throughput-sequencing htslib nim nim-lang
Last synced: 11 Mar 2025
https://github.com/brentp/echtvar
using all the bits for echt rapid variant annotation and filtering
genetic-variants genomics variant-analysis variant-annotations
Last synced: 04 Apr 2025
https://github.com/brentp/bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
Last synced: 09 Apr 2025
https://github.com/brentp/peddy
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
ancestry bioinformatics genomics genotype pedigree vcf
Last synced: 07 Apr 2025
https://github.com/brentp/jigv
igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
genomics genomics-visualization
Last synced: 11 Mar 2025
https://github.com/brentp/duphold
don't get DUP'ed or DEL'ed by your putative SVs.
genomics insanity structural-variation
Last synced: 11 Mar 2025
https://github.com/brentp/combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
Last synced: 16 Mar 2025
https://github.com/brentp/slurmpy
submit jobs to slurm with quick-and-dirty python
Last synced: 03 Apr 2025
https://github.com/brentp/vcfgo
a golang library to read, write and manipulate files in the variant call format.
Last synced: 04 Apr 2025
https://github.com/brentp/fishers_exact_test
Fishers Exact Test for Python (Cython)
Last synced: 07 Apr 2025
https://github.com/brentp/xopen
open files for buffered reading and writing in #golang
Last synced: 16 Mar 2025
https://github.com/brentp/rare-disease-wf
(WIP) best-practices workflow for rare disease
genomics rare-disease variants
Last synced: 11 Mar 2025
https://github.com/brentp/interlap
fast, pure-python interval overlap testing
Last synced: 16 Mar 2025
https://github.com/brentp/seqcover
seqcover allows users to view coverage for hundreds of genes and dozens of samples
genomics genomics-visualization hacktoberfest
Last synced: 11 Mar 2025
https://github.com/brentp/hts-nim-tools
useful command-line tools written to showcase hts-nim
bam bioinformatics genomics nim nim-lang vcf vcf-filtering
Last synced: 11 Mar 2025
https://github.com/brentp/hts-python
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
bam bioinformatics fasta genomics htslib python sam
Last synced: 21 Mar 2025
https://github.com/brentp/irelate
Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang
Last synced: 16 Mar 2025
https://github.com/brentp/combined-pvalues
combining p-values using modified stouffer-liptak for spatially correlated results (probes)
Last synced: 16 Mar 2025
https://github.com/brentp/bsub
python wrapper to submit jobs to bsub (and later qsub)
Last synced: 16 Mar 2025
https://github.com/brentp/tiwih
simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.
Last synced: 11 Mar 2025
https://github.com/brentp/cigar
simple library for dealing with SAM cigar strings
Last synced: 16 Mar 2025
https://github.com/brentp/indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
genome-assembly genomics k-mer-counting local-assembly nim-lang variant-calling vcf
Last synced: 11 Mar 2025
https://github.com/brentp/450k-analysis-guide
A Practical (And Opinionated) Guide To Analyzing 450K Data
Last synced: 11 Mar 2025
https://github.com/brentp/geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
Last synced: 06 May 2025
https://github.com/brentp/poverlap
significance testing over interval overlaps
Last synced: 21 Mar 2025
https://github.com/brentp/quicksect
a cythonized, extended version of the interval search tree in bx
Last synced: 21 Mar 2025
https://github.com/brentp/fraguracy
overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites
Last synced: 21 Mar 2025
https://github.com/brentp/vcfassoc
perform genotype-phenotype-association tests on a VCF with logistic regression.
Last synced: 14 Feb 2025
https://github.com/brentp/hts-zig
ziglang + htslib
bioinformatics genomics hacktoberfest htslib zig ziglang
Last synced: 14 Feb 2025
https://github.com/brentp/bw-python
python wrapper to dpryan79's bigwig library using cffi
Last synced: 14 Feb 2025
https://github.com/brentp/bigwig-nim
command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig
bigbed bigwig genomics high-throughput-sequencing nim nim-lang
Last synced: 14 Apr 2025
https://github.com/brentp/methylcode
Alignment and Tabulation of BiSulfite Treated Reads
Last synced: 14 Feb 2025
https://github.com/brentp/python-giggle
python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.
Last synced: 14 Feb 2025
https://github.com/brentp/tnsv
add true-negative SVs from a population callset to a truth-set.
Last synced: 11 Mar 2025
https://github.com/brentp/genoiser
use the noise
bioinformatics genomics high-throughput-sequencing nim nim-lang
Last synced: 14 Apr 2025
https://github.com/brentp/spacepile
convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
deep-learning genomics sequence-alignment
Last synced: 14 Feb 2025
https://github.com/brentp/aclust
streaming, flexible agglomerative clustering
Last synced: 14 Feb 2025
https://github.com/brentp/gobio
miscellaneous script-like stuff in go for bioinformatics
Last synced: 14 Feb 2025
https://github.com/brentp/bwa-mips
Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit
Last synced: 14 Feb 2025
https://github.com/brentp/bix
tabix file access with golang using biogo machinery
Last synced: 14 Feb 2025
https://github.com/brentp/gobe
a fast, interactive, light-weight, customizable, web-based comparative genomics viewer with simple text input format.
Last synced: 11 Mar 2025
https://github.com/brentp/clinical-components
Summarize the clinical (or lab) components and correlations of your dataset.
Last synced: 14 Feb 2025
https://github.com/brentp/inheritance
inheritance models for mendelian diseases
Last synced: 14 Feb 2025
https://github.com/brentp/bamject
DO NOT USE inject variants (snps/indels) from a vcf into a bam efficiently.
Last synced: 11 Mar 2025
https://github.com/brentp/skidmarks
find runs (non-randomness) in sequences
Last synced: 14 Feb 2025
https://github.com/brentp/bowfast
run bowtie then bfast on colorspace reads.
Last synced: 14 Feb 2025
https://github.com/brentp/falas
Fragment-Aware Local Assembly for Short-reads
assembly dna genomics structural-variation
Last synced: 14 Feb 2025
https://github.com/brentp/crystal
find clusters and model correlated data from DNA methylation and other genomic sources.
Last synced: 14 Feb 2025
https://github.com/brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
bam cram genomics genomics-visualization high-throughput-sequencing structural-variation
Last synced: 11 Mar 2025
https://github.com/brentp/go-blosc
go wrapper for blosc (blocked number compression with fast random access)
Last synced: 14 Feb 2025
https://github.com/brentp/nim-gzfile
simple reader and writer for gzipped (and regular) files
Last synced: 14 Apr 2025
https://github.com/brentp/celltypes450
adjust for cell-type composition in 450K data using houseman's and other methods.
Last synced: 14 Feb 2025
https://github.com/brentp/clustermodel
fitting models to clustered correlated data
Last synced: 14 Feb 2025
https://github.com/brentp/kexpr-nim
nim wrapper for Heng Li's kexpr math expression evaluator library
evaluator math math-expressions nim-lang
Last synced: 14 Feb 2025
https://github.com/brentp/pedfile
pedigree file parsing and relatedness calculations for nim
bioinformatics genomics pedigree
Last synced: 11 Mar 2025
https://github.com/brentp/shuffler
shuffle genome regions to determine probability of user-defined metric
Last synced: 05 Apr 2025
https://github.com/brentp/d4-nim
nim-lang wrapper for https://github.com/38/d4-format
bioinformatics genomics high-throughput-sequencing
Last synced: 11 Mar 2025
https://github.com/brentp/simplebed-rs
a simple bed file reader and writer that allows querying when an index is present
Last synced: 16 May 2025
https://github.com/brentp/bedder-rs
an API for intersections of genomic data
bam bed bioinformatics cram genomics vcf
Last synced: 14 Feb 2025
https://github.com/brentp/variantkey-nim
nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64
Last synced: 05 Apr 2025
https://github.com/brentp/bedder-py-wrappers
rust->python wrappers to be used by bedder
Last synced: 16 May 2025
https://github.com/brentp/find_cns
find conserved non-coding sequences (CNS)
Last synced: 23 Apr 2025
https://github.com/brentp/nim-cgranges
nim wrapper for https://github.com/lh3/cgranges for faster interval tree
Last synced: 11 Mar 2025
https://github.com/brentp/flatfeature
python module for dealing with BED format for genomic data as a numpy array.
Last synced: 11 Mar 2025
https://github.com/brentp/ksw2-nim
nim wrapper for lhs/ksw2 for fast smith-waterman
Last synced: 11 Mar 2025