An R package to time somatic mutations
☆66Dec 12, 2020Updated 5 years ago
Alternatives and similar repositories for MutationTimeR
Users that are interested in MutationTimeR are comparing it to the libraries listed below
Sorting:
- ☆84Apr 17, 2025Updated 10 months ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Jan 15, 2020Updated 6 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆47Apr 16, 2021Updated 4 years ago
- Testing a neutral evolution model on cancer sequencing data☆10Feb 17, 2021Updated 5 years ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆44Apr 16, 2021Updated 4 years ago
- Classifying tumor types based on Whole Genome Sequencing (WGS) data☆49Nov 20, 2023Updated 2 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆32Feb 18, 2026Updated last week
- Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data☆67Dec 25, 2022Updated 3 years ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆232May 15, 2025Updated 9 months ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆72May 23, 2024Updated last year
- Model-based tumour subclonal deconvolution using population genetics☆35Dec 2, 2025Updated 3 months ago
- 🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R htt…☆158Dec 25, 2025Updated 2 months ago
- A framework to infer mutational signatures in cancer over time☆56Jul 9, 2019Updated 6 years ago
- ☆76Jul 12, 2023Updated 2 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆18Jan 31, 2024Updated 2 years ago
- GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data a…☆21Aug 22, 2025Updated 6 months ago
- ASCAT R package☆199Feb 12, 2026Updated 2 weeks ago
- Mutational signature analysis for low statistics SNV data☆64Aug 7, 2024Updated last year
- Battenberg R package for subclonal copynumber estimation☆95Feb 20, 2026Updated last week
- Whole genome workflows☆12Nov 9, 2024Updated last year
- Inferring selection in cancer sequencing data using ABC and population based simulations☆12Jan 31, 2021Updated 5 years ago
- An R package to plot maps of clone distributions in somatic evolution☆19Jan 8, 2024Updated 2 years ago
- Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data…☆17Mar 6, 2024Updated last year
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Apr 7, 2022Updated 3 years ago
- SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational pattern…☆52Feb 8, 2026Updated 3 weeks ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆35Jan 28, 2022Updated 4 years ago
- Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids☆30Aug 8, 2023Updated 2 years ago
- SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations o…☆117Feb 8, 2026Updated 3 weeks ago
- Fast method for inferring cancer clonal population structure from SNV data.☆66Jan 20, 2026Updated last month
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆158Feb 12, 2026Updated 2 weeks ago
- R package to do enrichment analysis for neoantigens☆13Feb 21, 2022Updated 4 years ago
- A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)☆30Aug 30, 2019Updated 6 years ago
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆150Sep 9, 2020Updated 5 years ago
- SV clustering☆31Jul 5, 2021Updated 4 years ago
- CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …☆15Nov 28, 2023Updated 2 years ago
- Somatic copy variant caller (CNV) for next generation sequencing☆75Sep 12, 2024Updated last year
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆42Aug 21, 2025Updated 6 months ago
- Annotates variants in MAF with OncoKB annotation.☆141Feb 19, 2026Updated last week
- R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after cor…☆32Oct 29, 2025Updated 4 months ago