zhangwl's Stars
satijalab/seurat
R toolkit for single cell genomics
maehrlab/thymusatlastools
R package to accompany our recent Immunity paper on the mouse thymus developmental cell atlas.
lmcinnes/umap
Uniform Manifold Approximation and Projection
Japrin/STARTRAC
STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)
Japrin/sscClust
simpler single cell RNAseq data clustering
fritzsedlazeck/Sniffles
Structural variation caller using third generation sequencing
gerstung-lab/MutationTimeR
An R package to time somatic mutations
gerstung-lab/preAML
Code accompanying Prediction of AML risk in healthy individuals by Abelson, Collord, et al. (2018), Nature, 559:400-404
genepattern/GISTIC_2.0
Genomic Identification of Significant Targets in Cancer
NCBI-Hackathons/Community_Software_Tools_for_NGS
PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
raerose01/deconstructSigs
deconstructSigs
abyzovlab/CNVnator
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
raphael-group/THetA
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 repository includes the updated algorithm, called THetA2.
chrisamiller/RMEmod
A tool for discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors
baezortega/mutree
A pipeline for phylogenetic tree inference and mutation recurrence discovery
collinmelton/RecurrentMutationStats
This contains code for statistical analysis of recurrent mutations in whole genome sequencing data.
lixiangchun/decipherMutationalSignatures
Deciphering mutational signatures with alternative algorithms
TojalLab/signeR
RCollins13/CNView
Visualization and annotation of CNVs from population-scale whole-genome sequencing data
griffithlab/GenVisR
Genome data visualizations
macarthur-lab/igv_utils
utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
griffithlab/pVAC-Seq
DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
kartong88/Plot-Mutation-Landscape
A R code to generate a mutational signature plot