PeeperLab / CopywriteR
DNA copy number detection from off-target sequence data
☆31Updated 6 years ago
Alternatives and similar repositories for CopywriteR:
Users that are interested in CopywriteR are comparing it to the libraries listed below
- 📊Evaluating, filtering, comparing, and visualising VCF☆27Updated 2 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
- ☆34Updated 5 years ago
- ☆13Updated 7 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆70Updated 11 months ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Main repository for Drews et al. (Nature, 2022)☆39Updated last year
- Dirichlet Process based methods for subclonal reconstruction of tumours☆29Updated last month
- Comprehensive genome-wide visualization of absolute copy number and copy neutral variations☆29Updated 6 years ago
- DriverPower☆26Updated 3 months ago
- An R package for predicting HR deficiency from mutation contexts☆28Updated 2 months ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- ChIP-seq DC and QC Pipeline☆34Updated 4 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆30Updated last year
- Filtering of PDX samples for mouse derived reads☆27Updated 2 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…☆44Updated 2 years ago
- Mutational signature analysis for low statistics SNV data☆63Updated 8 months ago
- MutSig2CV from Lawrence et al. 2014☆31Updated 4 years ago
- ☆19Updated 7 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- processes GoT amplicon data and generates a table of metrics☆29Updated 2 years ago
- Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post…☆26Updated 8 months ago
- A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay☆15Updated 4 years ago
- a peak-calling and differential analysis tool for replicated ChIP-Seq data☆37Updated 2 years ago
- Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data☆34Updated 4 months ago
- Utility functions for FACETS☆35Updated last year
- a parallel R package for detecting copy-number alterations from short sequencing reads☆23Updated 3 years ago
- Filters for false-positive mutation calls in NGS☆30Updated 6 years ago
- ☆44Updated 6 years ago
- allele specific DNA methylation haplotype region☆14Updated last year