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| SomaticSignatures-package | SomaticSignatures package |
| dfConvertColumns | Utility functions |
| extractSignatures | Estimate Somatic Signatures |
| findSignatures | Estimate Somatic Signatures |
| gcContent | GC Content |
| grangesPlain | GRanges converter functions |
| hs-chrs | Human Chromosome Names |
| hsAllosomes | Human Chromosome Names |
| hsAutosomes | Human Chromosome Names |
| hsLinear | Human Chromosome Names |
| hsToplevel | Human Chromosome Names |
| k3we | Kmer datasets |
| k3wg | Kmer datasets |
| kmeansSignatures | Estimate Somatic Signatures |
| kmerFrequency | Kmer Frequency |
| kmers | Kmer datasets |
| kmers-data | Kmer datasets |
| mutational-normalization | Normalize Somatic Motifs |
| mutational-plots | Mutational Plots |
| mutational-signatures | Estimate Somatic Signatures |
| mutationContext | mutationContext functions |
| mutationContextH5vc | mutationContext functions |
| mutationContextMatrix | Estimate Somatic Signatures |
| mutationContextMutect | mutationContext functions |
| mutationDistance | Distributions of mutational locations. |
| ncbi | GRanges converter functions |
| nmfSignatures | Estimate Somatic Signatures |
| normalizeMotifs | Normalize Somatic Motifs |
| pcaSignatures | Estimate Somatic Signatures |
| plotRainfall | Distributions of mutational locations. |
| plotSampleMap | Estimate Somatic Signatures |
| plotSamples | Estimate Somatic Signatures |
| plotSamplesObserved | Estimate Somatic Signatures |
| plotSignatureMap | Estimate Somatic Signatures |
| plotSignatures | Estimate Somatic Signatures |
| plotVariantAbundance | Mutational Plots |
| readMutect | readMutect |
| seqchar | GRanges converter functions |
| SomaticSignatures | SomaticSignatures package |
| ucsc | GRanges converter functions |
| variants-utils | Utility functions |