DOI: 10.18129/B9.bioc.YAPSA    

This is the development version of YAPSA; for the stable release version, see YAPSA.

Yet Another Package for Signature Analysis

Bioconductor version: Development (3.11)

This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided to enable SNV and INDEL signature analysis.

Author: Daniel Huebschmann, Lea Jopp-Saile, Zuguang Gu and Matthias Schlesner

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

Citation (from within R, enter citation("YAPSA")):


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

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script 1. Usage of YAPSA
HTML R Script 2. Signature analysis with signature-specific cutoffs
HTML R Script 3. Indel signature analysis
HTML index.html
PDF   Reference Manual
Text   NEWS


biocViews BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 1.13.1
In Bioconductor since BioC 3.4 (R-3.3) (3 years)
License GPL-3
Depends R (>= 3.6.0), GenomicRanges, ggplot2, grid
Imports lsei, 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
Suggests testthat, BiocStyle, knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package YAPSA_1.13.1.tar.gz
Windows Binary YAPSA_1.13.1.zip
Mac OS X 10.11 (El Capitan) YAPSA_1.13.1.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/
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