S4Vectors (>= 0.16.0), Rsamtools (>= 1.30.0), rtracklayer (>=
1.38.0), robustbase (>= 0.92-8), SummarizedExperiment (>=
1.8.0)

Tumor Mutation Detection in Plasma using Barcoding
Yves Rozenholc [cre, aut]
Oddmund Nordgård [con, aut]
Nicolas Pécuchet [con]
Pierre-Laurent Puig [con]
Aims at detecting single nucleotide variation
(SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used
as a surrogate marker for tumor, at each base position of an Next Generation
Sequencing (NGS) analysis using barcoding. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.
This package has been used for Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) <https://www.nature.com/articles/s41598-022-09698-5>.

Visualization of Plasmid Profile Results
person("Adrian", "Zetner", email = "adrian.zetner@phac-aspc.gc.ca", role = c("aut", "cre"))
Contains functions developed to combine the results of querying a plasmid database using
short-read sequence typing with the results of a blast analysis against the query results.
ape, dendextend, dplyr, gdata, ggdendro, ggplot2, grid,
gridExtra, gtable, htmlwidgets, magrittr, plotly, plyr,
RColorBrewer, reshape2, RGraphics, rmarkdown, stringr

ape, dplyr, gdata, ggdendro, ggplot2, grid, gridExtra, gtable,
htmlwidgets, magrittr, plotly, plyr, RColorBrewer, reshape2,
stringr

Jessica M. Franklin, Younathan Abdia, Shirley V. Wang.
Creates realistic simulated datasets for causal inference based on a user-supplied example study, Franklin JM, Schneeweiss S, Polinski JM, and Rassen JA (2014) <doi:10.1016/j.csda.2013.10.018>.
It samples units from the data with replacement, and then simulates the exposure, the outcome, or both, based on the observed covariate values in the real data.
mgcv(>= 1.8-12), glm2(>= 1.1.2), nlme(>= 3.1-128), survival(>=
2.40-1), MASS, arm, lme4, twang, gbm, lattice, splines,
parallel, survey, grid, Matrix, xtable, latticeExtra,
RColorBrewer, epiDisplay, foreign, nnet