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| 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 |