amcpherson / citup
Clonality inference in multiple tumor samples using phylogeny
☆13Updated 7 years ago
Alternatives and similar repositories for citup:
Users that are interested in citup are comparing it to the libraries listed below
- ☆13Updated 7 years ago
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- Spatial Computational Inference of MEtastatic Timing (SCIMET)☆14Updated 5 years ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆34Updated 9 months ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆30Updated last year
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Updated 6 years ago
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆17Updated 5 years ago
- ☆19Updated 7 years ago
- ☆34Updated 5 years ago
- Fork of the Polysolver project☆31Updated 5 years ago
- An R package for predicting HR deficiency from mutation contexts☆28Updated 2 months ago
- ☆28Updated last year
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆31Updated 3 years ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated 4 months ago
- An R package to time somatic mutations☆61Updated 4 years ago
- ☆24Updated 5 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆70Updated 10 months ago
- Benchmarking of CNV calling tools☆18Updated 5 years ago
- Utility functions for FACETS☆35Updated last year
- QDNAseq package for Bioconductor☆49Updated 8 months ago
- Tutorial for STAR-Fusion, FusionInspector, and de novo reconstruction of fusion transcripts using Trinity☆14Updated 5 years ago
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆14Updated 9 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated 2 years ago
- Microsatellite instability (MSI) detection for cfDNA samples.☆19Updated 4 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 3 weeks ago
- Codes and Data for FFPEsig manuscript☆16Updated last year
- High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants☆22Updated 5 years ago
- MutSig2CV from Lawrence et al. 2014☆31Updated 4 years ago
- A tool for sample swap identification in high throughput sequencing studies☆10Updated last month
- ☆16Updated 6 years ago