Top 35 cancer-genomics open source projects

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

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

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

An ensemble approach to accurately detect somatic mutations using SomaticSeq

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

identifying mutational significance in cancer genomes

Python package to annotate and visualize gene fusions.

Snakemake-based workflow for detecting structural variants in WGS data

Unix, R and python tools for genomics and data science

cBioPortal for Cancer Genomics

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

Web client for CIViC: Clinical Interpretations of Variants in Cancer

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…

REVOLVER - Repeated Evolution in Cancer

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

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

Genomics using open source tools, running on GCP or AWS

Cancer Predisposition Sequencing Reporter (CPSR)

Backend server for Genome Nexus

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

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

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

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Backend Server for CIViC Project

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.

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

Single-cell copy number calling and event history reconstruction.

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)