An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
☆73May 23, 2024Updated 2 years ago
Alternatives and similar repositories for Palimpsest
Users that are interested in Palimpsest are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A framework to infer mutational signatures in cancer over time☆58Jul 9, 2019Updated 6 years ago
- Inferring selection in cancer sequencing data using ABC and population based simulations☆12Jan 31, 2021Updated 5 years ago
- Testing a neutral evolution model on cancer sequencing data☆10Feb 17, 2021Updated 5 years ago
- ☆86Apr 17, 2025Updated last year
- Bayesian mixture models for estimating and clustering cancer cell fractions☆26Dec 20, 2022Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- R package containing useful functions for mutational signature analysis☆86Updated this week
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆150Sep 9, 2020Updated 5 years ago
- Utility functions for FACETS☆40Oct 24, 2025Updated 7 months ago
- An R package to time somatic mutations☆71Dec 12, 2020Updated 5 years ago
- This repository contains the source code of the revised version of MutPanning. MutPanning is publicly available under the BSD3-Clause ope…☆13Nov 12, 2019Updated 6 years ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆235May 15, 2025Updated last year
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆162Feb 12, 2026Updated 3 months ago
- Decrypting somatic mutation patterns to reveal the evolution of cancer☆57Mar 10, 2021Updated 5 years ago
- DriverPower☆26Jan 18, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Framework for Metastatic And Clonal History INtegrative Analysis☆37Mar 5, 2021Updated 5 years ago
- Code accompanying The Evolutionary history of 2,658 cancers☆48Apr 16, 2021Updated 5 years ago
- SV clustering☆31Jul 5, 2021Updated 4 years ago
- Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ra…☆13Sep 15, 2023Updated 2 years ago
- R package for extracting and visualizing mutational patterns in base substitution catalogues☆107Nov 22, 2022Updated 3 years ago
- Model-based tumour subclonal deconvolution using population genetics☆36Dec 2, 2025Updated 6 months ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆53May 20, 2022Updated 4 years ago
- ☆79Jul 12, 2023Updated 2 years ago
- deconstructSigs☆144Apr 24, 2023Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data☆67Dec 25, 2022Updated 3 years ago
- HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jo…☆72Mar 19, 2026Updated 2 months ago
- Search for activating regulatory variants in the tumor genome☆15Apr 11, 2025Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆101Apr 20, 2021Updated 5 years ago
- Somatic copy variant caller (CNV) for next generation sequencing☆78Sep 12, 2024Updated last year
- 🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R htt…☆162Dec 25, 2025Updated 5 months ago
- R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after cor…☆32Oct 29, 2025Updated 7 months ago
- Battenberg R package for subclonal copynumber estimation☆97May 11, 2026Updated 3 weeks ago
- Predicting oncogenic potential of gene fusions☆13Feb 13, 2016Updated 10 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …☆161Jun 18, 2024Updated last year
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆44Apr 16, 2021Updated 5 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆25May 2, 2018Updated 8 years ago
- Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec☆13Aug 25, 2020Updated 5 years ago
- An R package for predicting HR deficiency from mutation contexts☆30Feb 13, 2025Updated last year
- ☆37Jul 28, 2019Updated 6 years ago
- CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …☆15Nov 28, 2023Updated 2 years ago