cancer-genomics

Unix, R and python tools for genomics and data science

cBioPortal for Cancer Genomics

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

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

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

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

Chromosome visualization for the web

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

Personal Cancer Genome Reporter (PCGR)

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Lollipop-style mutation diagrams for annotating genetic variations.

A visualization grammar and GPU-accelerated toolkit for genomic data

Haplotype-aware CNV analysis from single-cell RNA-seq

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 SigProfilerMatrixGenerator and SigProfilerPlotting.

Microassembly based somatic variant caller for NGS data

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

React Frontend of cBioPortal 🎉

What you need to process the Quarterly DepMap-Omics releases from Terra

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.