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
Alternatives and similar repositories for sequenza:
Users that are interested in sequenza are comparing it to the libraries listed below
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆30Updated last year
- DriverPower☆26Updated 2 months ago
- ☆13Updated 7 years ago
- Utility functions for FACETS☆35Updated 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
- Clonality inference in multiple tumor samples using phylogeny☆13Updated 7 years ago
- Codes and Data for FFPEsig manuscript☆16Updated last year
- Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec☆13Updated 4 years ago
- Clonality Inference in Multiple Tumor Samples using Phylogeny☆14Updated 9 years ago
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated 3 weeks ago
- Workflow for Sequenza, cellularity and ploidy☆18Updated 2 weeks 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
- Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data…☆16Updated last year
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 6 years ago
- All-FIT - Allele-Frequency-based Imputation of Tumor Purity☆17Updated 5 years ago
- Fork of the Polysolver project☆31Updated 5 years ago
- A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…☆31Updated 3 years ago
- Full-spectrum copy number variation detection by high-throughput DNA sequencing☆37Updated 3 years ago
- ☆19Updated 7 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 6 years ago
- An R package for predicting HR deficiency from mutation contexts☆28Updated 2 months ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆26Updated 6 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 4 years ago
- ☆19Updated 3 years ago
- BISulfite-seq CUI Toolkit☆19Updated 4 months 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
- ☆34Updated 5 years ago
- a parallel R package for detecting copy-number alterations from short sequencing reads☆23Updated 3 years ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated 4 months ago