Battenberg R package for subclonal copynumber estimation
☆95Feb 20, 2026Updated last month
Alternatives and similar repositories for battenberg
Users that are interested in battenberg are comparing it to the libraries listed below
Sorting:
- ASCAT R package☆199Feb 12, 2026Updated last month
- Battenberg algorithm and associated implementation script☆53Oct 21, 2020Updated 5 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆32Feb 18, 2026Updated last month
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆71Nov 20, 2020Updated 5 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆44Aug 24, 2022Updated 3 years ago
- A framework to infer mutational signatures in cancer over time☆56Jul 9, 2019Updated 6 years ago
- dN/dS methods to quantify selection in cancer and somatic evolution☆232May 15, 2025Updated 10 months ago
- ☆12Sep 22, 2025Updated 6 months ago
- ☆27Feb 9, 2026Updated last month
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆42Aug 21, 2025Updated 7 months ago
- ☆12Apr 26, 2020Updated 5 years ago
- Model-based tumour subclonal deconvolution using population genetics☆35Dec 2, 2025Updated 3 months ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆100Apr 20, 2021Updated 4 years ago
- Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)☆17Jan 15, 2020Updated 6 years ago
- ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal pa…☆12Apr 18, 2025Updated 11 months ago
- MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.☆59Mar 23, 2025Updated last year
- DriverPower☆26Jan 18, 2025Updated last year
- Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes☆44Apr 16, 2021Updated 4 years ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆22Dec 14, 2021Updated 4 years ago
- An R package to time somatic mutations☆67Dec 12, 2020Updated 5 years ago
- Application for inferring subclonal composition and evolution from whole-genome sequencing data.☆114Oct 12, 2022Updated 3 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
- 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
- SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer sampl…☆64Apr 24, 2025Updated 10 months ago
- Code accompanying The Evolutionary history of 2,658 cancers☆47Apr 16, 2021Updated 4 years ago
- Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.☆203Mar 20, 2024Updated 2 years ago
- SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations o…☆119Feb 8, 2026Updated last month
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆150Sep 9, 2020Updated 5 years ago
- Create timecourse "fish plots" that show changes in the clonal architecture of tumors☆173Jan 28, 2026Updated last month
- ☆85Apr 17, 2025Updated 11 months ago
- Python function for TMB snake plots☆16Feb 12, 2026Updated last month
- Repository of the TRanslational ONCOlogy library, which includes various algorithms (such as CAPRESE and CAPRI) and the Pipeline for Canc…☆30Mar 9, 2026Updated 2 weeks ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆72May 23, 2024Updated last year
- cDriver R package for finding candidate driver genes in cancers☆18Jan 18, 2018Updated 8 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 2 years ago
- Software program for checking sample matching for NGS data☆138Jun 20, 2024Updated last year
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- An R package for inferring the subclonal architecture of tumors☆122Mar 15, 2026Updated last week
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Jul 19, 2024Updated last year