Package: SomaticSignatures 2.43.0

Julian Gehring

SomaticSignatures: Somatic Signatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

Authors:Julian Gehring

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SomaticSignatures.pdf |SomaticSignatures.html✨
SomaticSignatures/json (API)
NEWS

# Install 'SomaticSignatures' in R:

install.packages('SomaticSignatures', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/juliangehring/somaticsignatures/issues

Datasets:

k3we - Kmer datasets
k3wg - Kmer datasets
sca_mm - SomaticCancerAlterations Results
sca_motifs_tiny - SomaticCancerAlterations Results
signatures21 - 21 Signatures
sigs_nmf - SomaticCancerAlterations Results
sigs_pca - SomaticCancerAlterations Results

On BioConductor:SomaticSignatures-2.43.0(bioc 3.21)SomaticSignatures-2.42.0(bioc 3.20)

sequencing somaticmutation visualization clustering genomicvariation statisticalmethod

6.85 score 22 stars 1 packages 54 scripts 421 downloads 32 mentions 37 exports 162 dependencies

Last updated 22 days agofrom:f592f53356. Checks:OK: 1 NOTE: 1 ERROR: 2 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	ERROR	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	ERROR	Oct 31 2024

Exports:assessNumberSignatures clusterSpectrum fitted gcContent hsAllosomes hsAutosomes hsLinear hsToplevel identifySignatures kmerFrequency motifMatrix mutationContext mutationContextMutect mutationDistance ncbi nmfDecomposition nmfSignatures normalizeMotifs observed pcaDecomposition pcaSignatures plotFittedSpectrum plotMutationSpectrum plotNumberSignatures plotObservedSpectrum plotRainfall plotSampleMap plotSamples plotSignatureMap plotSignatures plotVariantAbundance readMutect samples seqchar show signatures ucsc

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray dichromat digest doParallel dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats glue graph gridBase gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme NMF nnet openssl OrganismDbi patchwork pcaMethods pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics proxy purrr R6 rappdirs RBGL RColorBrewer Rcpp RCurl registry reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

SomaticSignatures

Rendered fromSomaticSignatures-vignette.Rhtmlusingknitr::knitron Oct 31 2024.

Last update: 2017-03-14
Started: 2014-03-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cluster Mutational Spectrum	cluster-spectrum clusterSpectrum
Decomposition Functions for Somatic Signatures	decomposition-signatures nmfDecomposition nmfSignatures pcaDecomposition pcaSignatures
GC Content	gcContent
GRanges converter functions	ncbi seqchar ucsc
Human Chromosome Names	hs-chrs hsAllosomes hsAutosomes hsLinear hsToplevel
Kmer Frequency	kmerFrequency
Kmer datasets	k3we k3wg kmers kmers-data
Group somatic moticfs	motifMatrix
Distributions of mutational locations.	mutationDistance plotRainfall
Normalize Somatic Motifs	mutational-normalization normalizeMotifs
Mutational Plots	mutational-plots plotVariantAbundance
Estimate Somatic Signatures	findSignatures identifySignatures mutational-signatures
'MutationalSignatures' class and methods	fitted fitted,MutationalSignatures-method MutationalSignatures MutationalSignatures-class observed observed,MutationalSignatures-method samples samples,MutationalSignatures-method show show,MutationalSignatures-method signatures signatures,MutationalSignatures-method
mutationContext functions	mutationContext mutationContextMutect
Number of Signatures	assessNumberSignatures plotNumberSignatures
readMutect	readMutect
SomaticCancerAlterations Results	sca-data sca_mm sca_motifs_tiny sca_sigs sigs_nmf sigs_pca
Plot Mutational Signatures	plotFittedSpectrum plotMutationSpectrum plotObservedSpectrum plotSampleMap plotSamples plotSignatureMap plotSignatures
21 Signatures	signatures21 signatures21-data
SomaticSignatures package	SomaticSignatures-package SomaticSignatures
Utility functions	dfConvertColumns variants-utils