Discover brentp/skidmarks Open Source project

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Python
License
MIT License
Created about 10 years ago
Updated over 6 years ago

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find runs (non-randomness) in sequences

cyvcf2

cython + htslib == fast VCF and BCF processing

Cython

366

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

332

goleft

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

202

slivar

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

Nim

189

smoove

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

187

bio-playground

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

181

somalier

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

Nim

180

hts-nim

nim wrapper for htslib for parsing genomics data files

Nim

149

cruzdb

python access to UCSC genomes database

Python

129

peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Jupyter Notebook

122

bwa-meth

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

Python

116

jigv

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

Nim

107

echtvar

using all the bits for echt rapid variant annotation and filtering

Rust

105

combat.py

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

Python

intintmap

fast int64-int64 map for go

duphold

don't get DUP'ed or DEL'ed by your putative SVs.

Nim

slurmpy

submit jobs to slurm with quick-and-dirty python

Python

pyfasta

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

Python

vcfgo

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

fishers_exact_test

Fishers Exact Test for Python (Cython)

Python

xopen

open files for buffered reading and writing in #golang

interlap

fast, pure-python interval overlap testing

Python

seqcover

seqcover allows users to view coverage for hundreds of genes and dozens of samples

Nim

rare-disease-wf

(WIP) best-practices workflow for rare disease

Nextflow

hts-python

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

Python

go-chartjs

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

hts-nim-tools

useful command-line tools written to showcase hts-nim

Nim

irelate

Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang

bsub

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

Python

combined-pvalues

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

Python

align

sequence alignment. global, local, glocal.

Python

bigly

a pileup library that embraces the huge

indelope

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

Nim

tiwih

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

Nim

cigar

simple library for dealing with SAM cigar strings

Python

gsort

sort genomic data

450k-analysis-guide

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

TeX

geneimpacts

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

Python

quicksect

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

Python

poverlap

significance testing over interval overlaps

Python

fastbit-python

pythonic access to fastbit

Python

nim-lapper

fast easy interval overlapping for nim-lang

Nim

lua-stringy

fast lua string operations

pybloomfaster

fast bloomfilter

vcfassoc

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

Python

toolshed

python stuff I use

Python

bw-python

python wrapper to dpryan79's bigwig library using cffi

methylcode

Alignment and Tabulation of BiSulfite Treated Reads

tnsv

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

Nim

hileup

horizontal pileup

nim-kmer

DNA kmer operations for nim

Nim

genoiser

use the noise

Nim

bigwig-nim

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig

Nim

vcf-bench

evaluating vcf parsing libraries

Zig

agoodle

numpy + GDAL == agoodle

Python

hts-zig

ziglang + htslib

Zig

aclust

streaming, flexible agglomerative clustering

Python

gobio

miscellaneous script-like stuff in go for bioinformatics

excord

extract SV signal from a BAM

fastahack-python

cython wrapper to fastahack

C++

spacepile

convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

Rust

bwa-mips

Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit

Python

gobe

a fast, interactive, light-weight, customizable, web-based comparative genomics viewer with simple text input format.

Haxe

bix

tabix file access with golang using biogo machinery

sveval

run multiple sv evalution tools

Python

clinical-components

Summarize the clinical (or lab) components and correlations of your dataset.

Python

bowfast

run bowtie then bfast on colorspace reads.

Shell

bcf

bcf parsing in golang

inheritance

inheritance models for mendelian diseases

Python

falas

Fragment-Aware Local Assembly for Short-reads

Nim

bamject

DO NOT USE inject variants (snps/indels) from a vcf into a bam efficiently.

Nim

bpbio

basepair bio: a single binary with many useful genomics subtools.

Nim

kexpr-nim

nim wrapper for Heng Li's kexpr math expression evaluator library

clustermodel

fitting models to clustered correlated data

Python

go-blosc

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

celltypes450

adjust for cell-type composition in 450K data using houseman's and other methods.

crystal

find clusters and model correlated data from DNA methylation and other genomic sources.

Python

variantkey-nim

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

pedfile

pedigree file parsing and relatedness calculations for nim

Nim

shuffler

shuffle genome regions to determine probability of user-defined metric

Python

go-giggle

golang wrapper to giggle

bedder-rs

an API for intersections of genomic data

Rust

nim-gzfile

simple reader and writer for gzipped (and regular) files

Nim

find_cns

find conserved non-coding sequences (CNS)

Python

nim-cgranges

nim wrapper for https://github.com/lh3/cgranges for faster interval tree

d4-nim

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

Nim

flatfeature

python module for dealing with BED format for genomic data as a numpy array.

Python

faidx

faidx for golang

tabix-py

interface to tabix using cffi

4bit

4bit fasta format.

ksw2-nim

nim wrapper for lhs/ksw2 for fast smith-waterman

htsuse

some C stuff that uses htslib

nim-minizip

nothing to see here.

pyfastx

unified access to fasta, fastx using kseq.h + ??

learnflash

all the stuff i want to remember how to do in haxe / flash

ififo

ififo provides a fast, sized, generic thread-safe FIFO in golang.

dotfiles

my .bash, .vim, .* files

Shell

cysolar

copy of pysolar using cython

Python

cgotbx

yeah, another tabix wrapper for go.

100

totable

simple python / cython wrapper to tokyo cabinet tables

brentp/skidmarks

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