Table 1 Feature comparison with other packages
From: MutationalPatterns: the one stop shop for the analysis of mutational processes
Group | Feature | MutationalPatterns v3.4.0 | MutationalPatterns v1.4.3 [12] | Sigprofiler [13] | SignatureAnalyzer [13] | deconstructSigs [14] | sparseSignatures [15] | signeR [16] | somaticSignatures [17] | Maftools [18] | decompTumor2Sig [19] |
|---|---|---|---|---|---|---|---|---|---|---|---|
Language | Language/platform | R (bioconductor) | R (bioconductor) | Python (+ R wrapper) | Python | R (cran) | R (bioconductor) | R (bioconductor) | R (bioconductor) | R (bioconductor) | R (bioconductor) |
Genome | Supported genomes | Genome agnostic | Genome agnostic | Human, Mice, Rat, Yeast | – | Human | Genome agnostic | Genome agnostic | Genome agnostic | Genome agnostic | Genome agnostic |
Mutation profile | 96 SNV profile | X | X | X | – | X | – | X | X | X | X |
|  | extended SNV profile | X | – | X | – | – | – | – | X | – | X |
|  | Indel profile | X | – | X | – | – | – | – | – | – | – |
|  | DBS profile | X | – | X | – | – | – | – | – | – | – |
|  | MBS profile | X | – | – | – | – | – | – | – | – | – |
|  | Transcriptional strand bias profile | X | X | X | – | – | – | – | – | – | – |
|  | Replicative strand bias profile | X | X | X | – | – | – | – | – | – | – |
|  | Pool samples | X | – | – | – | – | – | – | – | – | – |
Signature extraction | Signature extraction (NMF) | X | X | X | – | – | – | – | X | X | – |
|  | Signature extraction (Bayes NMF) | X | – | – | X | – | – | X | – | – | – |
|  | Signature extraction (Lasso NMF) | – | – | – | – | – | X | – | – | – | – |
|  | Update signature names | X | – | – | – | – | – | – | – | – | – |
Signature refitting | Signature refitting | X | X | X | X | X | – | – | – | – | X |
|  | Strict signature refitting | X | – | X | X | X | – | – | – | – | X |
|  | Strict signature refitting (best subset) | X | – | – | – | – | – | – | – | – | X |
– | Bootstrapped signature refitting | X | – | – | – | – | – | – | – | – | – |
|  | Correlation bootstrapped refitting | X | – | – | – | – | – | – | – | – | – |
Signature damage analysis | Signature potential damage analysis | X | – | – | – | – | – | – | – | – | – |
Signature other | Plot supported profiles / signatures | X | X | X | X | X | X | X | X | X | X |
|  | Plot and compare supported profiles | X | X | – | – | – | – | – | – | – | – |
|  | Signature contribution heatmap | X | X | – | – | – | – | X | X | – | – |
|  | Signature contribution barplot | X | X | – | – | – | – | X | X | – | – |
|  | Signature/profile similarity heatmap | X | X | – | – | – | – | – | – | X | – |
|  | Similarity with reconstructed profile barplot | X | – | – | – | – | – | – | – | – | – |
Genomic distribution | Rainfall plot | X | X | – | – | – | – | – | X | X | – |
|  | Enrichment/depletion in genomic region | X | X | – | – | – | – | – | – | – | – |
|  | Region specific profiles | X | – | – | – | – | – | – | – | – | – |
|  | Region specific signatures | X | – | – | – | – | – | – | – | – | – |
|  | Unsupervised regional similarity | X | – | – | – | – | – | – | – | – | – |
Lesion segregation | Lesion segregation | X | – | – | – | – | – | – | – | – | – |