Package: YAPSA Type: Package Title: Yet Another Package for Signature Analysis Version: 1.38.0 Date: 2025-11-28 Authors@R: c(person("Daniel", "Huebschmann", role = c("aut", "cre"), email = "huebschmann.daniel@googlemail.com"), person("Lea", "Jopp-Saile", role = "aut"), person("Carolin", "Andresen", role = "aut"), person("Zuguang", "Gu", role = "aut"), person("Matthias", "Schlesner", role = "aut")) Imports: limSolve, SomaticSignatures, VariantAnnotation, Seqinfo, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Description: 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. License: GPL-3 Suggests: testthat, BiocStyle, knitr, rmarkdown VignetteBuilder: knitr LazyLoad: yes biocViews: Sequencing, DNASeq, SomaticMutation, Visualization, Clustering, GenomicVariation, StatisticalMethod, BiologicalQuestion RoxygenNote: 7.2.3 Encoding: UTF-8 Config/pak/sysreqs: cmake libgmp3-dev make libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev libmpfr-dev libssl-dev perl xz-utils zlib1g-dev Repository: Bioconductor 3.23 Date/Publication: 2026-04-28 12:44:05 UTC RemoteUrl: https://github.com/bioc/YAPSA RemoteRef: RELEASE_3_23 RemoteSha: 1e00570307373c11f4375fc6aef8c96c36280933 NeedsCompilation: no Packaged: 2026-11-01 11:13:16 UTC; root Author: Daniel Huebschmann [aut, cre], Lea Jopp-Saile [aut], Carolin Andresen [aut], Zuguang Gu [aut], Matthias Schlesner [aut] Maintainer: Daniel Huebschmann