Brent Pedersen

Login: brentp

Company: University of Utah

Location: Salt Lake City, UT

Bio: Doing bioinformatics at University of Utah and hacking in python, go, C, bash, and nim.

Blog:

Blog:

Member of

1. null

Repositories

450k-analysis-guide

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

4bit

4bit fasta format.

aclust

streaming, flexible agglomerative clustering

aegea

Amazon Web Services Operator Interface

aFC

Calculates allelic Fold Change (aFC) using standard input files for fastQTL.

agoodle

numpy + GDAL == agoodle

align

sequence alignment. global, local, glocal.

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

bcf

bcf parsing in golang

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bcolz

A columnar data container that can be compressed.

bedtools

A powerful toolset for genome arithmetic.

bedtools2

A powerful toolset for genome arithmetic.

bedtools-python

A Python interface to the BEDTools API using Cython

bigly

a pileup library that embraces the huge

bigwig

bigwig in go via libbigWig

bioawk

BWK awk modified for biological data

biogo

biogo is a bioinformatics library for Go

bio-playground

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

bix

tabix file access with golang using biogo machinery

bootstrip

Resampling residuals of a linear model to determine significance with bootstrap-like sub-sampling

bowfast

run bowtie then bfast on colorspace reads.

bpbio

Automatically exported from code.google.com/p/bpbio

bpgeo

Automatically exported from code.google.com/p/bpgeo

brentp.github.com

null

brentp.github.io

blog hosting

bsub

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

bwa-meth

fast and accurate alignment of BS-Seq reads

bwa-mips

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

bw-python

python wrapper to dpryan79's bigwig library using cffi

celltypes450

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

cgotabix

quick-n-dirty tabix in go using cgo

cgotbx

yeah, another tabix wrapper for go.

chroma

Everything you want to do with colors, in nim.

cigar

simple library for dealing with SAM cigar strings

clinical-components

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

clustermodel

fitting models to clustered correlated data

clustermodelr

fit models to clustered, correlated data (R package)

cnvkit

Copy number variant detection from targeted DNA sequencing

CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

combat.py

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

combined-pvalues

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

conda

OS-agnostic, system-level binary package manager and ecosystem

crampex

cram reader in golang via system call to samtools

cruzdb

python access to UCSC genomes database

crystal

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

cysolar

copy of pysolar using cython

cyvcf2

cython + htslib == fast VCF and BCF processing

dotfiles

my .bash, .vim, .* files

easyssh

Golang package for easy remote execution through SSH (Fork enables cross-compile)

excord

extract SV signal from a BAM

faidx

faidx for golang

fastahack-python

cython wrapper to fastahack

fastbit-python

pythonic access to fastbit

find_cns

find conserved non-coding sequences (CNS)

fishers_exact_test

Fishers Exact Test for Python (Cython)

fixle

fast, fixed-length, integer-keyed db via tokyo-cabine

flatfeature

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

gargs

better(?) xargs in go

gemini

a lightweight db framework for disease and population genetics.

geneimpacts

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

mosfun

fast tabulation of alignment events

mosfun

fast tabulation of alignment events

ggd

null

ggd-hg38-recipes

data recipes for hg38

giggle

Interval data structure

go-athenaeum

a collection of small golang libraries I use

gobe

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

gobio

miscellaneous script-like stuff in go for bioinformatics

gobitmapbenchmark

A Go project to benchmark various bitmap implementations (this is not a library!)

go-blosc

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

go-chartjs

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

gocroaring

Go wrapper for CRoaring

go-datastructures

null

go-giggle

golang wrapper to giggle

goleft

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

golsh

Approximate Nearest Neighbors in Go

goluaez

ez embedding lua in go

go-stree

A package for Go that can be used for range queries on large number of intervals

gqt

A genotype query interface.

grabix

a wee tool for random access into BGZF files.

graphics

biogo genomic graphics repository

gsort

sort genomic data

gwiz

null

hapdip

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data

HipSTR

Genotype and phase short tandem repeats using Illumina whole-genome sequencing data

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

hts

biogo high throughput sequencing repository

hts-nim

nim wrapper for htslib for parsing genomics data files

hts-nim-tools

useful command-line tools written to show-case hts-nim

hts-python

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

htsuse

some C stuff that uses htslib

hugo-blog

not rendered content. ignore.

ififo

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

indelope

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

inheritance

inheritance models for mendelian diseases

interlap

fast, pure-python interval overlap testing

intintmap

fast int64-int64 map for go

irelate

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

kexpr-nim

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

learnflash

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

lsh

Locality Sensitive Hashing for Go (Multi-probe LSH, LSH Forest, basic LSH)

lua-stringy

a place for my lua projects

smoove

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

smoove

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

lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery

methylcode

Alignment and Tabulation of BiSulfite Treated Reads

mmslice

mmap file to array of integers in go

mosdepth

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

mosfun

fast tabulation of alignment events

mosfun

fast tabulation of alignment events

Nim

Nim is a compiled, garbage-collected systems programming language with a design that focuses on efficiency, expressiveness, and elegance (in the order of priority).

nim-kmer

DNA kmer operations for nim

nim-lapper

fast easy interval overlapping for nim-lang

nim-plotly

plotting library for nim-lang

nim-vla

Variable length arrays for Nim

packages

List of packages for Nimble

peddy

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

poretools

a toolkit for working with Oxford nanopore data

poverlap

significance testing over interval overlaps

power

null

primer

Primer is a Flash-like API built on top of Canvas using jQuery. (this fork aims to improve speed and make it easier to attach events to objects).

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

pybloomfaster

fast bloomfilter

pyfaidx

"samtools faidx" compatible FASTA indexing in pure python

pyfasta

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

pyfastx

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

python-giggle

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

quicksect

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

recipes

Conda recipes for the bioconda channel.

roaring

null

rstuff

R stuff I wrote

samtools

null

seqtk

Toolkit for processing sequences in FASTA/Q formats

shuffler

shuffle genome regions to determine probability of user-defined metric

skidmarks

find runs (non-randomness) in sequences

slurmpy

submit jobs to slurm with quick-and-dirty python

smoove

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

smoove

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

sorted-random-go

generate sorted random numbers in #golang

svtools

Tools for processing and analyzing structural variants.

svtyper

Bayesian genotyper for structural variants

synstats

code for synstats.appspot.com

tabix-py

interface to tabix using cffi

toolshed

python stuff I use

totable

simple python / cython wrapper to tokyo cabinet tables

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

vcfassoc

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

vcfgo

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

xopen

open files for buffered reading and writing in #golang

Commits To