cBioPortal for Cancer Genomics

Unix, R and python tools for genomics and data science

React Frontend of cBioPortal 🎉

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

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

Chromosome visualization for the web

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

Lollipop-style mutation diagrams for annotating genetic variations.

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

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 SigProfilerMatrixGen…

An ensemble approach to accurately detect somatic mutations using SomaticSeq

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

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

Personal Cancer Genome Reporter (PCGR)

Backend server for Genome Nexus

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

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.

Snakemake-based workflow for detecting structural variants in genomic data

Microassembly based somatic variant caller for NGS data

Backend Server for CIViC Project