chrisamiller / copyCatLinks
a parallel R package for detecting copy-number alterations from short sequencing reads
☆23Updated 4 years ago
Alternatives and similar repositories for copyCat
Users that are interested in copyCat are comparing it to the libraries listed below
Sorting:
- DriverPower☆26Updated 9 months ago
- Flexible Bayesian inference of mutational signatures☆36Updated 2 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Updated 7 years ago
- novoBreak: local assembly for breakpoint detection in cancer genomes☆25Updated 7 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- Advanced plotting functions for CNV data generated by CNV-Seq and Control Freec☆13Updated 5 years ago
- Utility functions for FACETS☆39Updated last year
- 📊Evaluating, filtering, comparing, and visualising VCF☆28Updated 2 years ago
- Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter☆19Updated 7 years ago
- An R package for predicting HR deficiency from mutation contexts☆29Updated 8 months ago
- DRAGEN Tumor/Normal workflow post-processing☆22Updated 2 years ago
- GTEx analysis scripts☆20Updated 8 years ago
- a peak-calling and differential analysis tool for replicated ChIP-Seq data☆36Updated 3 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆31Updated 2 years ago
- MSKCC Reis-Filho Lab pipeline thingy☆17Updated last month
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 6 years ago
- ☆26Updated last year
- Filters for false-positive mutation calls in NGS☆34Updated 6 years ago
- highly-efficient & lightweight mutation signature matrix aggregation☆19Updated 3 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆71Updated last year
- Codes and Data for FFPEsig manuscript☆17Updated last year
- A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data☆16Updated 5 years ago
- This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…☆18Updated last year
- Dirichlet Process based methods for subclonal reconstruction of tumours☆30Updated 7 months ago
- A set of tools to annotate VCF files with expression and readcount data☆29Updated 7 months ago
- ☆35Updated 5 years ago
- Fork of https://bitbucket.org/mcgranahanlab/lohhla☆18Updated 5 years ago
- a Shiny/R application to view and annotate copy number variations☆28Updated 2 years ago
- ☆38Updated 4 years ago
- ☆25Updated 7 years ago