Imports: S4Vectors (>= 0.16.0), Rsamtools (>= 1.30.0), rtracklayer (>=
1.38.0), robustbase (>= 0.92-8), SummarizedExperiment (>=
GenomicRanges (>= 1.30.0), VariantAnnotation (>= 1.24.0)

Title: Tumor Mutation Detection in Plasma using Barcoding
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>.

Title: Visualization of Plasmid Profile Results
Authors@R: person("Adrian", "Zetner", email = "adrian.zetner@phac-aspc.gc.ca", role = c("aut", "cre"))
Description: 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.
Imports: ape, dendextend, dplyr, gdata, ggdendro, ggplot2, grid,
gridExtra, gtable, htmlwidgets, magrittr, plotly, plyr,
RColorBrewer, reshape2, RGraphics, rmarkdown, stringr

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

Author: Jessica M. Franklin, Younathan Abdia, Shirley V. Wang.
Description: 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.
2.40-1), MASS, arm, lme4, twang, gbm, lattice, splines,
parallel, survey, grid, Matrix, xtable, latticeExtra,

Title: Optimal Two-Period Multi-Arm Platform Design
c(person("Xiaomeng", "Yuan", , "xiaomeng.yuan@stjude.org", role = c("aut", "cre")),
person("Haitao", "Pan", , "Haitao.Pan@stjude.org", role = c("aut")))
Description: Design parameters can be calculated using this package based on the optimal two-period
multi-arm platform design allowing pre-planned deferred arms to be added during the trial. More
details about the design method can be found in the paper: Pan, H., Yuan, X. and Ye, J. (2022)
"An optimal two-period multi-arm platform design with adding new arms". Manuscript submitted for
publication. For additional references: Dunnett, C. W. (1955) <doi:10.2307/2281208>.
Suggests: knitr, rmarkdown, ggplot2, testthat (>= 3.0.0)