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archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

ascat

ASCAT copy number R package

bonemarrowmap

A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations

bsub

Send R code/R scripts/shell commands to LSF cluster without leaving R

cbioportaldata

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

cicero

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

cri_bioinformatics_workshop

Tutorials and code for CRI bioinformatics workshop.

gdc-docs

Official repository for GDC User Guides in Markdown format

genvisr

Genome data visualizations

mergebams

Command line tool for merging single cell rna-sequencing bams with intelligent tag preservation

meta_programs_tirosh

Repo to patch gene names from Tirosh Meta-Programs Paper

mjz1.github.io

ngs-tools-gatk

A Perl package containing an interface to the GATK suite of tools.

numbat

Haplotype-aware CNV analysis in scRNA-Seq

onclass

Single cell typing based on cell ontology

openondemandapps

pileup2base

Parse samtools pileup file to get how many bases and what kind of bases are called

rocker-versioned2

Run current & prior versions of R using docker. rocker/r-ver, rocker/rstudio, rocker/shiny, rocker/tidyverse, and so on.

rstudio-img

run_numbat

docker for numbat

run_phylo

SK HPF implementation of the phylowgs clonal evolution pipleine

scatools

Tools for processing scATAC data

sccna

scomatic

A tool for detecting somatic variants in single cell data

scrnamp

seurat

R toolkit for single cell genomics

single_cell_pipeline

Single Cell Analysis Automated Workflow

slurmr

slurmR: A Lightweight Wrapper for Slurm

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms