Inferring Somatic Signatures from Single Nucleotide Variant Calls | Table of Contents | 1 Motivation: The Concept Behind Mutational Signatures | 2 Methodology: From Mutations to Somatic Signatures | 3 Workflow: Analysis with the SomaticSignatures Package | 4 Use case: Estimating Somatic Signatures from TCGA WES Studies | 5 Alternatives: Inferring Somatic Signatures with Different Approaches | 6 Frequently Asked Questions | 7 References | References | 8 Session Information
Package: SomaticSignatures 2.49.0
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:
SomaticSignatures_2.49.0.tar.gz
SomaticSignatures_2.49.0.zip(r-4.7)SomaticSignatures_2.49.0.zip(r-4.6)SomaticSignatures_2.49.0.zip(r-4.5)
SomaticSignatures_2.49.0.tgz(r-4.6-any)SomaticSignatures_2.49.0.tgz(r-4.5-any)
SomaticSignatures_2.49.0.tar.gz(r-4.7-any)SomaticSignatures_2.49.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SomaticSignatures/json (API)
| # 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-2.49.0(bioc 3.24)SomaticSignatures-2.48.0(bioc 3.23)
sequencingsomaticmutationvisualizationclusteringgenomicvariationstatisticalmethod
Last updated from:4a8c707c3c. Checks:3 ERROR, 5 NOTE, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 301 | ||
| linux-devel-x86_64 | NOTE | 612 | ||
| source / vignettes | OK | 509 | ||
| linux-release-x86_64 | NOTE | 618 | ||
| macos-release-arm64 | ERROR | 435 | ||
| macos-oldrel-arm64 | ERROR | 340 | ||
| windows-devel | NOTE | 540 | ||
| windows-release | NOTE | 543 | ||
| windows-oldrel | NOTE | 546 | ||
| wasm-release | FAIL | 255 |
Exports:assessNumberSignaturesclusterSpectrumfittedgcContenthsAllosomeshsAutosomeshsLinearhsToplevelidentifySignatureskmerFrequencymotifMatrixmutationContextmutationContextMutectmutationDistancencbinmfDecompositionnmfSignaturesnormalizeMotifsobservedpcaDecompositionpcaSignaturesplotFittedSpectrumplotMutationSpectrumplotNumberSignaturesplotObservedSpectrumplotRainfallplotSampleMapplotSamplesplotSignatureMapplotSignaturesplotVariantAbundancereadMutectsamplesseqcharshowsignaturesucsc
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestdoParallelensembldbevaluatefarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggplot2gluegraphgridBasegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeNMFnnetopensslOrganismDbipcaMethodspkgconfigplyrpngProtGenericsproxyR6rappdirsRBGLRColorBrewerRcppRCurlregistryreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml
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 |