Brent Pedersen (@brentp)
github

brentp

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Top repositories

1

cyvcf2

cython + htslib == fast VCF and BCF processing
Cython
366
star
2

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
Go
332
star
3

goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
Go
202
star
4

slivar

genetic variant expressions, annotation, and filtering for great good.
Nim
189
star
5

smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Go
187
star
6

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
C
181
star
7

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Nim
180
star
8

hts-nim

nim wrapper for htslib for parsing genomics data files
Nim
149
star
9

cruzdb

python access to UCSC genomes database
Python
129
star
10

peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Jupyter Notebook
122
star
11

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
Python
116
star
12

jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
Nim
107
star
13

echtvar

using all the bits for echt rapid variant annotation and filtering
Rust
105
star
14

combat.py

python / numpy / pandas / patsy version of ComBat for removing batch effects.
Python
98
star
15

intintmap

fast int64-int64 map for go
Go
93
star
16

duphold

don't get DUP'ed or DEL'ed by your putative SVs.
Nim
90
star
17

slurmpy

submit jobs to slurm with quick-and-dirty python
Python
88
star
18

pyfasta

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
Python
86
star
19

vcfgo

a golang library to read, write and manipulate files in the variant call format.
Go
65
star
20

fishers_exact_test

Fishers Exact Test for Python (Cython)
Python
63
star
21

xopen

open files for buffered reading and writing in #golang
Go
60
star
22

interlap

fast, pure-python interval overlap testing
Python
50
star
23

seqcover

seqcover allows users to view coverage for hundreds of genes and dozens of samples
Nim
49
star
24

rare-disease-wf

(WIP) best-practices workflow for rare disease
Nextflow
49
star
25

hts-python

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
Python
49
star
26

go-chartjs

golang library to make https://chartjs.org/ plots (this is vanilla #golang, not gopherjs)
Go
47
star
27

hts-nim-tools

useful command-line tools written to showcase hts-nim
Nim
46
star
28

irelate

Streaming relation (overlap, distance, KNN) of (any number of) sorted genomic interval sets. #golang
Go
45
star
29

bsub

python wrapper to submit jobs to bsub (and later qsub)
Python
43
star
30

combined-pvalues

combining p-values using modified stouffer-liptak for spatially correlated results (probes)
Python
40
star
31

align

sequence alignment. global, local, glocal.
Python
40
star
32

bigly

a pileup library that embraces the huge
Go
39
star
33

indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)
Nim
39
star
34

tiwih

simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.
Nim
39
star
35

cigar

simple library for dealing with SAM cigar strings
Python
37
star
36

gsort

sort genomic data
Go
35
star
37

450k-analysis-guide

A Practical (And Opinionated) Guide To Analyzing 450K Data
TeX
34
star
38

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.
Python
31
star
39

quicksect

a cythonized, extended version of the interval search tree in bx
Python
30
star
40

poverlap

significance testing over interval overlaps
Python
29
star
41

fastbit-python

pythonic access to fastbit
Python
26
star
42

nim-lapper

fast easy interval overlapping for nim-lang
Nim
24
star
43

lua-stringy

fast lua string operations
C
21
star
44

pybloomfaster

fast bloomfilter
C
21
star
45

vcfassoc

perform genotype-phenotype-association tests on a VCF with logistic regression.
Python
20
star
46

toolshed

python stuff I use
Python
19
star
47

bw-python

python wrapper to dpryan79's bigwig library using cffi
C
19
star
48

methylcode

Alignment and Tabulation of BiSulfite Treated Reads
C
16
star
49

tnsv

add true-negative SVs from a population callset to a truth-set.
Nim
15
star
50

hileup

horizontal pileup
C
15
star
51

nim-kmer

DNA kmer operations for nim
Nim
15
star
52

genoiser

use the noise
Nim
15
star
53

bigwig-nim

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig
Nim
15
star
54

vcf-bench

evaluating vcf parsing libraries
Zig
14
star
55

agoodle

numpy + GDAL == agoodle
Python
13
star
56

hts-zig

ziglang + htslib
Zig
12
star
57

aclust

streaming, flexible agglomerative clustering
Python
12
star
58

gobio

miscellaneous script-like stuff in go for bioinformatics
Go
12
star
59

excord

extract SV signal from a BAM
Go
11
star
60

fastahack-python

cython wrapper to fastahack
C++
11
star
61

spacepile

convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.
Rust
10
star
62

bwa-mips

Map sequence from Molecular Inversion Probes with BWA, strip arms, de-dup, ..., profit
Python
10
star
63

gobe

a fast, interactive, light-weight, customizable, web-based comparative genomics viewer with simple text input format.
Haxe
10
star
64

bix

tabix file access with golang using biogo machinery
Go
9
star
65

sveval

run multiple sv evalution tools
Python
8
star
66

clinical-components

Summarize the clinical (or lab) components and correlations of your dataset.
Python
8
star
67

bowfast

run bowtie then bfast on colorspace reads.
Shell
7
star
68

bcf

bcf parsing in golang
Go
7
star
69

inheritance

inheritance models for mendelian diseases
Python
7
star
70

skidmarks

find runs (non-randomness) in sequences
Python
7
star
71

falas

Fragment-Aware Local Assembly for Short-reads
Nim
7
star
72

bamject

DO NOT USE inject variants (snps/indels) from a vcf into a bam efficiently.
Nim
7
star
73

bpbio

basepair bio: a single binary with many useful genomics subtools.
Nim
6
star
74

kexpr-nim

nim wrapper for Heng Li's kexpr math expression evaluator library
C
5
star
75

clustermodel

fitting models to clustered correlated data
Python
5
star
76

go-blosc

go wrapper for blosc (blocked number compression with fast random access)
Go
5
star
77

celltypes450

adjust for cell-type composition in 450K data using houseman's and other methods.
R
5
star
78

crystal

find clusters and model correlated data from DNA methylation and other genomic sources.
Python
5
star
79

variantkey-nim

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64
C
4
star
80

pedfile

pedigree file parsing and relatedness calculations for nim
Nim
4
star
81

shuffler

shuffle genome regions to determine probability of user-defined metric
Python
4
star
82

go-giggle

golang wrapper to giggle
Go
4
star
83

bedder-rs

an API for intersections of genomic data
Rust
4
star
84

nim-gzfile

simple reader and writer for gzipped (and regular) files
Nim
4
star
85

find_cns

find conserved non-coding sequences (CNS)
Python
4
star
86

nim-cgranges

nim wrapper for https://github.com/lh3/cgranges for faster interval tree
C
3
star
87

d4-nim

nim-lang wrapper for https://github.com/38/d4-format
Nim
3
star
88

flatfeature

python module for dealing with BED format for genomic data as a numpy array.
Python
3
star
89

faidx

faidx for golang
Go
3
star
90

tabix-py

interface to tabix using cffi
C
3
star
91

4bit

4bit fasta format.
C
3
star
92

ksw2-nim

nim wrapper for lhs/ksw2 for fast smith-waterman
C
3
star
93

htsuse

some C stuff that uses htslib
C
2
star
94

nim-minizip

nothing to see here.
C
2
star
95

pyfastx

unified access to fasta, fastx using kseq.h + ??
C
2
star
96

learnflash

all the stuff i want to remember how to do in haxe / flash
2
star
97

ififo

ififo provides a fast, sized, generic thread-safe FIFO in golang.
Go
2
star
98

dotfiles

my .bash, .vim, .* files
Shell
2
star
99

cysolar

copy of pysolar using cython
Python
2
star
100

cgotbx

yeah, another tabix wrapper for go.
Go
1
star