Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.UCSC.hg38, data.table, dplyr, GenomeInfoDb,
GenomicRanges, graphics, grDevices, IRanges, RColorBrewer,
stats, stringi, utils

Biostrings, BSgenome, data.table, dplyr, GenomeInfoDb,
GenomicRanges, graphics, grDevices, IRanges, RColorBrewer,
stats, stringi, utils, zip

Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" catalogs
of mutational spectra or signatures.

In-Depth Characterization and Analysis of Mutational Signatures
('ICAMS')
Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Imperialist Competitive Algorithm for Optimal Designs
c(person("Ehsan", "Masoudi", role = c("aut", "cre"),  email = "ehsan.masoudi@wwu.de"),  person("Heinz", "Holling", role = "aut"),  person("Weng Kee", "Wong", role = "aut"))
Finding locally D-optimal, minimax D-optimal, standardized maximin D-optimal, optim-on-the-average and multiple objective optimal designs for nonlinear models. Different Fisher information matrices can also be set by user. There are also  useful functions for verifying the optimality of the designs with respect to different criteria by equivalence theorem. ICA is a meta-heuristic evolutionary algorithm inspired from the socio-political process of humans. See Masoudi et al. (2016) <doi:10.1016/j.csda.2016.06.014>.
Rcpp, Rsolnp, nloptr, stats, graphics, grDevices
Ehsan Masoudi [aut, cre],
Heinz Holling [aut],
Weng Kee Wong [aut]