Unix, R and python tools for genomics and data science

cBioPortal for Cancer Genomics

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

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

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Chromosome visualization for the web

Personal Cancer Genome Reporter (PCGR)

Lollipop-style mutation diagrams for annotating genetic variations.

Microassembly based somatic variant caller for NGS data

Training and evaluating a variational autoencoder for pan-cancer gene expression data

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

An ensemble approach to accurately detect somatic mutations using SomaticSeq

microsatellite instability detection using tumor only or paired tumor-normal data

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

Web client for CIViC: Clinical Interpretations of Variants in Cancer

identifying mutational significance in cancer genomes

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

REVOLVER - Repeated Evolution in Cancer

React Frontend of cBioPortal 🎉

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

Backend Server for CIViC Project

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

An interactive and collaborative graphical curation tool for cancer pathways

Python package to annotate and visualize gene fusions.

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

Snakemake-based workflow for detecting structural variants in WGS data

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

A novel management, annotation, and machine learning framework for analyzing cancer mutations