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

Personal Cancer Genome Reporter (PCGR)

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

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

REVOLVER - Repeated Evolution in Cancer

Cancer Predisposition Sequencing Reporter (CPSR)

ConsensusTME Gene Sets and R Script

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

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

R wrapper for utilizing the SigProfilerMatrixGenerator framework

An R wrapper for SigProfilerExtractor that 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 o…

ESTIMATE tumor infiltration, the tidy way

Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec

Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/

Bioconductor R-package: Curated Prostate Cancer Data

scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

An R wrapper for running the SigProfilerPlotting framework

A database for microRNA-gene/protein expression correlation in cancer.