39 open source projects by brentp

cython + htslib == fast VCF and BCF processing

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

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

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

nim wrapper for htslib for parsing genomics data files

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

python access to UCSC genomes database

plotting library for nim-lang

variant expressions, annotation, and filtering for great good.

open files for buffered reading and writing in #golang

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

golang library to make https://chartjs.org/ plots (this is vanilla #golang, not gopherjs)

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

perform genotype-phenotype-association tests on a VCF with logistic regression.

fast easy interval overlapping for nim-lang

Alignment and Tabulation of BiSulfite Treated Reads

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

annotate a VCF with other VCFs/BEDs/tabixed files

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.

sequence alignment. global, local, glocal.

fast bloomfilter

(WIP) best-practices workflow for rare disease

echt rapid variant annotation and filtering

sort genomic data

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

find large indels (in the blind spot between GATK/freebayes and SV callers)

better(?) xargs in go

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

simple library for dealing with SAM cigar strings

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

A Practical (And Opinionated) Guide To Analyzing 450K Data

pythonic access to fastbit

fast int64-int64 map for go

use the noise

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

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

a pileup library that embraces the huge

numpy + GDAL == agoodle