cancer-genomics

Unix, R and python tools for genomics and data science

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

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

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

Personal Cancer Genome Reporter (PCGR)

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

Lollipop-style mutation diagrams for annotating genetic variations.

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Microassembly based somatic variant caller for NGS data

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

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

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

identifying mutational significance in cancer genomes

REVOLVER - Repeated Evolution in Cancer

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

Web client for CIViC: Clinical Interpretations of Variants in Cancer

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

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

Cancer Predisposition Sequencing Reporter (CPSR)

Python package to annotate and visualize gene fusions.

Snakemake-based workflow for detecting structural variants in WGS data

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

Backend Server for CIViC Project

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