cancerit / CaVEManLinks
SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
☆63Updated 7 months ago
Alternatives and similar repositories for CaVEMan
Users that are interested in CaVEMan are comparing it to the libraries listed below
Sorting:
- Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.☆57Updated last year
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆53Updated 3 years ago
- ☆36Updated 6 years ago
- Battenberg algorithm and associated implementation script☆53Updated 5 years ago
- SV clustering☆31Updated 4 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆72Updated 5 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 6 years ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆43Updated 4 years ago
- Opossum is a tool to pre-process RNA-seq reads prior to variant calling.☆28Updated 7 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…☆45Updated 3 years ago
- An R package for predicting HR deficiency from mutation contexts☆30Updated 10 months ago
- Identifying recurrent mutations in cancer☆39Updated 4 years ago
- ☆69Updated 3 years ago
- ☆46Updated 6 years ago
- Documenting usage and experience with bioinformatic tools☆40Updated 10 years ago
- Cloud-based single-cell copy-number variation analysis tool☆53Updated 2 years ago
- Collection of CGAT NGS Pipelines☆43Updated 7 years ago
- ☆21Updated 2 weeks ago
- Battenberg R package for subclonal copynumber estimation☆92Updated this week
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆72Updated last year
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆49Updated 6 years ago
- Multi-sample somatic variant caller☆52Updated 3 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 9 years ago
- SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA☆27Updated 5 years ago
- Quality of RNA-Seq Toolset☆53Updated 6 years ago
- Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests☆50Updated last year
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆98Updated 4 years ago
- Filters for false-positive mutation calls in NGS☆34Updated 6 years ago
- ☆72Updated 2 years ago
- Concordance and contamination estimator for tumor–normal pairs☆58Updated last year