FunGeST / Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
☆70Updated 10 months ago
Alternatives and similar repositories for Palimpsest:
Users that are interested in Palimpsest are comparing it to the libraries listed below
- An R package to time somatic mutations☆61Updated 4 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- ☆13Updated 7 years ago
- An R package for predicting HR deficiency from mutation contexts☆28Updated 2 months ago
- R package containing useful functions for mutational signature analysis☆80Updated last week
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 3 weeks ago
- Rocking R at UMCCR☆9Updated 4 years ago
- ☆38Updated 5 years ago
- Utility functions for FACETS☆34Updated last year
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆34Updated 9 months ago
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆41Updated 4 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 3 years ago
- Battenberg R package for subclonal copynumber estimation☆86Updated last week
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 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…☆44Updated 2 years ago
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Updated 6 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated 2 years ago
- QDNAseq package for Bioconductor☆49Updated 8 months ago
- MutSig2CV from Lawrence et al. 2014☆31Updated 4 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆30Updated last year
- ☆43Updated 6 years ago
- Mutational signature analysis for low statistics SNV data☆63Updated 8 months ago
- Somatic copy variant caller (CNV) for next generation sequencing☆70Updated 7 months ago
- Genomic Identification of Significant Targets in Cancer (GISTIC), version 2☆51Updated 3 years ago
- A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays☆30Updated last year
- Filtering of PDX samples for mouse derived reads☆27Updated 2 years ago
- Burden testing against public controls☆50Updated last year
- ☆34Updated 5 years ago
- Clonality inference in multiple tumor samples using phylogeny☆13Updated 7 years ago