🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

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

Clone identification from single-cell data

Multi-sample somatic variant caller

Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation

An R package for mutation quality control of cancer genomic sequening dataset

Datasets and analysis results released with the REVOLVER package for Cancer Evolution.

Tumour clone trees for subclonal deconvolution from bulk sequencing data

Tumour-in-normal contamination assessment for tumour-matched-normal assays

📦 An R package for inferring the mutational exposures difference between groups.

R Shiny based lightweight mutation exploration tool

a Nextflow ACE-Seq calling and annotation pipeline based on DKFZ-ODCF/ACEseqWorkflow

Tumour mutation trees for subclonal deconvolution from bulk sequencing data

Bayesian inference of gene mutant dosage from targeted panels without matched normal

Searching, downloading and analysing relevant data from the MSK-CHORD cohort

Pseudo-timing copy number alterations in cancer

This repo contains an R package to execute ROKET's real data analysis workflow on TCGA cancer types

A computational framework to quantify individual-level NMD efficiency and assess its variability across human tissues, tumors and individuals using RNA-seq and WES data