R toolkit for single cell genomics

R package to accompany our recent Immunity paper on the mouse thymus developmental cell atlas.

Uniform Manifold Approximation and Projection

STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)

simpler single cell RNAseq data clustering

Structural variation caller using third generation sequencing

An R package to time somatic mutations

Code accompanying Prediction of AML risk in healthy individuals by Abelson, Collord, et al. (2018), Nature, 559:400-404

Genomic Identification of Significant Targets in Cancer

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

deconstructSigs

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

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This re…

A tool for discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

A pipeline for phylogenetic tree inference and mutation recurrence discovery

This contains code for statistical analysis of recurrent mutations in whole genome sequencing data.

Deciphering mutational signatures with alternative algorithms

Visualization and annotation of CNVs from population-scale whole-genome sequencing data

Genome data visualizations

utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.

DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools

A R code to generate a mutational signature plot