cran / sequenza
This is a read-only mirror of the CRAN R package repository. sequenza — Copy Number Estimation from Tumor Genome Sequencing Data. Homepage: https://sequenzatools.bitbucket.io, Mailing list: https://groups.google.com/forum/#!forum/sequenza-user-group Report bugs for this package: https://bitbucket.org/sequenzatools/sequenza/issues
☆18Updated 5 years ago
Related projects ⓘ
Alternatives and complementary repositories for sequenza
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆17Updated 5 years ago
- Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec☆13Updated 4 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆29Updated last year
- ☆13Updated 7 years ago
- Workflow for Sequenza, cellularity and ploidy☆17Updated 4 months ago
- Clonality inference in multiple tumor samples using phylogeny☆13Updated 7 years ago
- Main repository for Drews et al. (Nature, 2022)☆37Updated last year
- DriverPower☆26Updated 4 months ago
- Utility functions for FACETS☆34Updated 7 months ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆33Updated 4 months ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Updated last year
- ☆25Updated 8 months ago
- knowledge-based genotyping of cancer hotspots from the tumor BAM files☆19Updated 2 years ago
- CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-frien…☆18Updated 4 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated last month
- 📊Evaluating, filtering, comparing, and visualising VCF☆27Updated last year
- A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)☆29Updated 5 years ago
- High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants☆21Updated 4 years ago
- MutSig2CV from Lawrence et al. 2014☆30Updated 4 years ago
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆13Updated 9 years ago
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆30Updated 3 years ago
- A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations☆35Updated 2 years ago
- Codes and Data for FFPEsig manuscript☆15Updated 9 months ago
- ☆33Updated 5 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆26Updated 6 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- ☆19Updated 3 years ago
- Model-based subclonal deconvolution from bulk sequencing.☆33Updated last year
- An R package for predicting HR deficiency from mutation contexts☆27Updated last year