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Table 1 MutationalPatterns feature overview and comparison with related software tools

From: MutationalPatterns: comprehensive genome-wide analysis of mutational processes

Functionality Analysis Mutational
pmsignature [23] MutSpec [36] Somatic
Signatures [37]
deconstructSigs [35] EMu [38]
  Language/platform R R Galaxy R R C++
Mutational characteristics Mutation spectrum X X X X X
Transcriptional strand bias X X
96 mutation profile X X X X
Mutational signatures Signature extraction (NMF) X X X X
Signature extraction (NMF) with strand bias X X
Signature contribution heatmap X X
Signature contribution barplot X X X X
Hierarchical sample clustering based on signature contribution X X X
Signature similarity heatmap X X
Plot and compare two 96 profiles X X
Sample signature similarity heatmap X
Find optimal linear combination of known signatures X X
Genomic distribution Rainfall plot/mutation clustering along the genome X X
Enrichment/depletion in genomic regions X X