YAPSA
Yet Another Package for Signature Analysis
Bioconductor version: Release (3.19)
This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.
Author: Daniel Huebschmann [aut], Lea Jopp-Saile [aut], Carolin Andresen [aut], Zuguang Gu [aut, cre], Matthias Schlesner [aut]
Maintainer: Zuguang Gu <z.gu at dkfz.de>
citation("YAPSA")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("YAPSA")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("YAPSA")| 1. Usage of YAPSA | HTML | R Script |
| 2. Signature-specific cutoffs | HTML | R Script |
| 3. Confidence Intervals | HTML | R Script |
| 4. Stratified Analysis of Mutational Signatures | HTML | R Script |
| 5. Indel signature analysis | HTML | R Script |
| 6. Usage of YAPSA for WES data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0), GenomicRanges, ggplot2, grid |
| Imports | limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils |
| System Requirements | |
| URL |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | YAPSA_1.30.0.tar.gz |
| Windows Binary (x86_64) | YAPSA_1.30.0.zip (64-bit only) |
| macOS Binary (x86_64) | YAPSA_1.30.0.tgz |
| macOS Binary (arm64) | YAPSA_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/YAPSA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/YAPSA |
| Bioc Package Browser | https://code.bioconductor.org/browse/YAPSA/ |
| Package Short Url | https://bioconductor.org/packages/YAPSA/ |
| Package Downloads Report | Download Stats |