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mSigPlot - Plotting Mutational Signatures and Mutational Spectra

Plotting functions for mutational signatures and mutational spectra, including single base substitutions (SBS), doublet base substitutions (DBS), and small insertions and deletions (indels). Generates plots similar to those used previously in Alexandrov et al. (2020)<doi:10.1038/s41586-020-1943-3> and Rozen et al. (2026)<doi:10.5281/zenodo.18451842>.

Last updated

5.46 score 36 scripts 135 downloads

cosmicsig - Mutational Signatures from COSMIC (Catalogue of Somatic Mutations in Cancer)

A data package with 2 main package variables: 'signature' and 'etiology'. The 'signature' variable contains the latest mutational signature profiles released on COSMIC <https://cancer.sanger.ac.uk/signatures/> for 3 mutation types: * Single base substitutions in the context of preceding and following bases, * Doublet base substitutions, and * Small insertions and deletions. 'cosmicsig' stands for COSMIC signatures. Please run ?'cosmicsig' for more information.

Last updated

3.24 score 1 stars 35 scripts 633 downloads

mSigTools - Mutational Signature Analysis Tools

Utility functions for mutational signature analysis as described in Alexandrov, L. B. (2020) <doi:10.1038/s41586-020-1943-3>. This package provides two groups of functions. One is for dealing with mutational signature "exposures" (i.e. the counts of mutations in a sample that are due to each mutational signature). The other group of functions is for matching or comparing sets of mutational signatures. 'mSigTools' stands for mutational Signature analysis Tools.

Last updated

3.18 score 2 stars 15 scripts 174 downloads

fastrc - Fast Reverse Complement of DNA and RNA Sequences

Fast reverse complement of DNA and RNA sequences using a 'C++' lookup table for O(1) per-base complement mapping. Supports full IUPAC ambiguity codes, DNA and RNA modes, case preservation, and NA handling. Much faster than other packages for computing reverse complements of many short sequences such as primers, probes, and, k-mers.

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cpp

3.00 score 3 scripts 125 downloads