genome / scicloneView external linksLinks
An R package for inferring the subclonal architecture of tumors
☆121Oct 13, 2023Updated 2 years ago
Alternatives and similar repositories for sciclone
Users that are interested in sciclone are comparing it to the libraries listed below
Sorting:
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆149Sep 9, 2020Updated 5 years ago
- Create timecourse "fish plots" that show changes in the clonal architecture of tumors☆171Jan 28, 2026Updated 2 weeks ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆53May 20, 2022Updated 3 years ago
- CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk …☆15Nov 28, 2023Updated 2 years ago
- Model-based tumour subclonal deconvolution using population genetics☆34Dec 2, 2025Updated 2 months ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆231May 15, 2025Updated 8 months ago
- Battenberg R package for subclonal copynumber estimation☆95Dec 8, 2025Updated 2 months ago
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆42Aug 21, 2025Updated 5 months ago
- Probabilistic model for inferring clonal population structure from deep NGS sequencing.☆118Aug 19, 2020Updated 5 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆32Mar 21, 2025Updated 10 months ago
- A framework to infer mutational signatures in cancer over time☆56Jul 9, 2019Updated 6 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Apr 16, 2019Updated 6 years ago
- Visualization tool for temporal clonal evolution.☆18Mar 13, 2020Updated 5 years ago
- R package for extracting and visualizing mutational patterns in base substitution catalogues☆107Nov 22, 2022Updated 3 years ago
- ASCAT R package☆199Updated this week
- Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data☆67Dec 25, 2022Updated 3 years ago
- Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.☆484Jan 27, 2026Updated 2 weeks ago
- Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberration…☆76Aug 20, 2021Updated 4 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆72May 23, 2024Updated last year
- Use gene expression to predict phenotype sample information☆19Feb 13, 2018Updated 8 years ago
- Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.☆158Jan 29, 2026Updated 2 weeks ago
- Code accompanying The Evolutionary history of 2,658 cancers☆47Apr 16, 2021Updated 4 years ago
- Application for inferring subclonal composition and evolution from whole-genome sequencing data.☆113Oct 12, 2022Updated 3 years ago
- CONICS: COpy-Number analysis In single-Cell RNA-Sequencing☆76Feb 27, 2023Updated 2 years ago
- Fast method for inferring cancer clonal population structure from SNV data.☆66Jan 20, 2026Updated 3 weeks ago
- Genome data visualizations☆220Jan 10, 2026Updated last month
- Multi-sample cancer phylogeny reconstruction☆36Oct 19, 2017Updated 8 years ago
- Analysis pipeline for cancer sequencing data☆112Apr 30, 2025Updated 9 months ago
- Precision HLA typing from next-generation sequencing data☆208Mar 5, 2024Updated last year
- Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.☆70Aug 22, 2021Updated 4 years ago
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆44Apr 16, 2021Updated 4 years ago
- Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…☆42Apr 18, 2024Updated last year
- Battenberg algorithm and associated implementation script☆53Oct 21, 2020Updated 5 years ago
- An R package to time somatic mutations☆65Dec 12, 2020Updated 5 years ago
- Bayesian mixture models for estimating and clustering cancer cell fractions☆24Dec 20, 2022Updated 3 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆100Apr 20, 2021Updated 4 years ago
- Clonality inference in multiple tumor samples using phylogeny☆13Sep 12, 2017Updated 8 years ago
- Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R☆12Dec 6, 2021Updated 4 years ago
- Software program for checking sample matching for NGS data☆137Jun 20, 2024Updated last year