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