cancerit / cgpBattenberg
Battenberg algorithm and associated implementation script
☆52Updated 4 years ago
Alternatives and similar repositories for cgpBattenberg:
Users that are interested in cgpBattenberg are comparing it to the libraries listed below
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- Battenberg R package for subclonal copynumber estimation☆85Updated last month
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 3 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆52Updated 4 years ago
- Quality of RNA-Seq Toolset☆52Updated 5 years ago
- Mutational signature analysis for low statistics SNV data☆63Updated 7 months ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆70Updated 10 months ago
- OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data☆50Updated 2 weeks ago
- An R package for inferring the subclonal architecture of tumors☆117Updated last year
- R package containing useful functions for mutational signature analysis☆80Updated last week
- ☆67Updated last year
- Workflows for converting between sequence data formats☆38Updated 3 years ago
- ☆78Updated 11 years ago
- nucleosome calling using ATAC-seq☆106Updated 4 years ago
- Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay☆56Updated 3 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆97Updated 2 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- R package designed to simplify structural variant analysis☆72Updated 3 years ago
- An R package for predicting HR deficiency from mutation contexts☆28Updated last month
- 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…☆43Updated 2 years ago
- R package for bcbio RNA-seq analysis.☆62Updated 6 months ago
- HMMRATAC peak caller for ATAC-seq data☆100Updated 4 months ago
- Inferring and visualizing clonal evolution in multi-sample cancer sequencing☆146Updated 4 years ago
- Relevant papers for CNV and SV approaches☆94Updated 4 months ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 5 years ago
- An R package to time somatic mutations☆61Updated 4 years ago
- BISulfite-seq CUI Toolkit☆65Updated 2 months ago
- ☆71Updated 10 months ago
- Characterization of Germline variants☆98Updated 3 years ago