DOI: 10.18129/B9.bioc.decompTumor2Sig  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see decompTumor2Sig.

Decomposition of individual tumors into mutational signatures by signature refitting

Bioconductor version: 3.16

Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

Author: Rosario M. Piro [aut, cre], Sandra Krueger [ctb]

Maintainer: Rosario M. Piro <rmpiro at>

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biocViews BiologicalQuestion, BiomedicalInformatics, DNASeq, Genetics, GenomicVariation, SNP, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 2.14.0
In Bioconductor since BioC 3.9 (R-3.6) (4 years)
License GPL-2
Depends R (>= 4.0), ggplot2
Imports methods, Matrix, quadprog (>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl
Suggests knitr, rmarkdown, BiocStyle
Depends On Me
Imports Me musicatk
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