theboocock

theboocock's Stars

• ossu/bioinformatics

  :microscope: Path to a free self-taught education in Bioinformatics!

  5.6k36624938

• nextflow-io/nextflow

  A DSL for data-driven computational pipelines

  Language:Groovy2.8k893.4k642

• thomasp85/gganimate

  A Grammar of Animated Graphics

  Language:R2k59454309

• Factual/drake

  Data workflow tool, like a "Make for data"

  Language:Clojure1.5k151188110

• lh3/seqtk

  Toolkit for processing sequences in FASTA/Q formats

  Language:C1.4k62176307

• DataBiosphere/toil

  A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

  Language:Python904563k240

• nservant/HiC-Pro

  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

  Language:Python39018610181

• broadinstitute/pilon

  Pilon is an automated genome assembly improvement and variant detection tool

  Language:Scala3442917060

• szymonmaszke/vimpyter

  Edit your Jupyter notebooks in Vim/Neovim

  Language:Vim Script334132317

• arq5x/lumpy-sv

  lumpy: a general probabilistic framework for structural variant discovery

  Language:C31627332119

• iqtree/iqtree2

  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

  Language:C++2581524358

• genome/pindel

  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

  Language:C++164548590

• hakyimlab/PrediXcan

  PrediXcan Project

  Language:Python107181158

• weisslj/cpp-argparse

  NOT YET: Python's excellent ArgumentParser in C++

  Language:C++727017

• joepickrell/fgwas

  Functional genomics and genome-wide association studies

  Language:C++65101113

• cc2qe/vawk

  An awk-like VCF parser

  Language:Python5571412

• gkichaev/PAINTOR_V3.0

  Fast, integrative fine mapping with functional data

  Language:C++5576420

• arq5x/bedtools-python

  A Python interface to the BEDTools API using Cython

  Language:C28509

• JosephCrispell/homoplasyFinder

  A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

  Language:R193243

• smangul1/UMI-Reducer

  A computational tool for processing and differentiating PCR duplicates from biological duplicates

  Language:Python102191

• hall-lab/long-read-validation

  Long-read validation of BEDPE structural variation

  Language:Python9513

• SiminaB/Fdr-regression

  Code for "A direct approach to estimating false discovery rates conditional on covariates" by SM Boca and JT Leek

  Language:TeX6402

• johnlees/tajima-D

  calculates tajima's D from bcftools query input

  Language:C++432

• boonelab/sgatools

  Language:HTML3342

• bvilhjal/phensim

  Code snippets for phenotype and genotype simulations...

  Language:Python3201

• TomKellyGenetics/heatmap.2x

  Enhancements to Heatmap.2 from the gplots R package

  Language:R3211

• amzurita/VariantCallingYeast_Kruglyak

  Variant calling pipeline for yeast samples

  Language:Shell110

• theboocock/coco

  Correlation conditional analysis.

  Language:R1205

• theboocock/COTOR

  Fast, integrative colocalisation mapping with functional data

  Language:C++1100

• theboocock/gwas-pw

  Pariwise analysis of GWAS

  Language:C++1101