There are 26 repositories under cancer-genomics topic.
Unix, R and python tools for genomics and data science
cBioPortal for Cancer Genomics
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.
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
Lollipop-style mutation diagrams for annotating genetic variations.
A visualization grammar and GPU-accelerated toolkit for genomic data
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Haplotype-aware CNV analysis from single-cell RNA-seq
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.
microsatellite instability detection using tumor only or paired tumor-normal data
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.
Snakemake-based workflow for detecting structural variants in genomic data
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
REVOLVER - Repeated Evolution in Cancer
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
Bioinformatics on GCP, AWS or Azure
Web client for CIViC: Clinical Interpretations of Variants in Cancer
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
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.
Identifying tumor cells at the single-cell level using machine learning