YAPSA

DOI: 10.18129/B9.bioc.YAPSA    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see YAPSA.

Yet Another Package for Signature Analysis

Bioconductor version: 3.12

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, Lea Jopp-Saile, Carolin Andresen, Zuguang Gu and Matthias Schlesner

Maintainer: Daniel Huebschmann <huebschmann.daniel at googlemail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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		index.html
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.4 (R-3.3) (4.5 years)
License	GPL-3
Depends	R (>= 3.6.0), GenomicRanges, ggplot2, grid
Imports	limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, PMCMR, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	YAPSA_1.16.0.tar.gz
Windows Binary	YAPSA_1.16.0.zip
macOS 10.13 (High Sierra)	YAPSA_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/YAPSA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/YAPSA
Package Short Url	https://bioconductor.org/packages/YAPSA/
Package Downloads Report	Download Stats