af8's Stars
mskcc/facets-suite
Utility functions for FACETS
anso-sertier/crisscross
aviari/wginr
WGInR ('Whole Genomes In R') are C and R tools from the Lyon Cancer Bioinformatics Facility to manipulate Whole Genomes in R.
brentp/slivar
genetic variant expressions, annotation, and filtering for great good.
dariober/cnv_facets
Somatic copy variant caller (CNV) for next generation sequencing
pachterlab/sleuth
Differential analysis of RNA-Seq
brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
lh3/seqtk
Toolkit for processing sequences in FASTA/Q formats
samtools/bcftools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
Illumina/strelka
Strelka2 germline and somatic small variant caller
nf-core/tools
Python package with helper tools for the nf-core community.
slzhao/QC3
QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
jennybc/here_here
I love the here package. Here's why.
jdblischak/singleCellSeq
Batch effects and the effective design of single-cell gene expression studies
aroneklund/jetset
An R package with one-to-one gene-probeset mappings for Affymetrix human microarrays
tgac-vumc/ACE
Absolute Copy Number Estimation using low-coverage whole genome sequencing data
kahun/awesome-sysadmin
A curated list of amazingly awesome open source sysadmin resources inspired by Awesome PHP.
clindet/rctl
A set of command line tools based on R and JavaScript.
zwdzwd/transvar
TransVar - multiway annotator for precision medicine
SciLifeLab/Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
bioconda/bioconda-recipes
Conda recipes for the bioconda channel.
atks/vt
A tool set for short variant discovery in genetic sequence data.
spotify/luigi
Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.
samtools/htslib
C library for high-throughput sequencing data formats
kevinblighe/EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labeling
seandavi/awesome-variant-databases
A collection of genomic variant databases
seandavi/awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
bedops/bedops
:microscope: BEDOPS: high-performance genomic feature operations
stevekm/reference-annotations
Makefile for reference annotations for genes & genomic regions
broadinstitute/gatk
Official code repository for GATK versions 4 and up