Table 1 MutationalPatterns feature overview and comparison with related software tools

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