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")))
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>.
knitr, rmarkdown, ggplot2, testthat (>= 3.0.0)
Xiaomeng Yuan [aut, cre],
Haitao Pan [aut]

Optimal Two-Period Multiarm Platform Design with New
Experimental Arms Added During the Trial
Design parameters of the optimal two-period multiarm platform design
(controlling for either family-wise error rate or pair-wise error rate) can be calculated
using this package, 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 multiarm platform design with new experimental arms added
during the trial". Manuscript submitted for publication. For additional references: Dunnett,
C. W. (1955) <doi:10.2307/2281208>.

Single-Cell Immune Repertoire and Gene Expression Analysis
We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology (Yermanos A, et al (2021) <doi:10.1093/nargab/lqab023>).
c(person("Alexander", "Yermanos", role = c("aut", "cre"), email = "ayermanos@gmail.com"),
person("Andreas", "Agrafiotis", role = "ctb"),
person("Raphael", "Kuhn", role = "ctb"),
person("Victor", "Kreiner", role = "ctb"),
person("Damiano", "Robbiani", role = "ctb"),
person("Josephine", "Yates", role = "ctb"),
person("Jiami", "Han", role = "ctb"),
person("Chrysa", "Papadopoulou", role = "ctb"),
person("Cédric", "Weber", role = "ctb"),
person("Danielle", "Shlesinger", role = "ctb"),
person("Raphael", "Dizerens", role = "ctb"))
BiocGenerics, Biostrings, dplyr, ggplot2, knitr, jsonlite,
Matrix, plyr, reshape2, rmarkdown, seqinr, Seurat,
SeuratObject, stringr, tibble, tidyr, utils, useful
AnnotationDbi, ape, circlize, cowplot, data.table,
doParallel, fda.usc, fgsea, ggrepel, ggridges, ggseqlogo, grid,
gridExtra, harmony, igraph, IRanges, limma, keras, methods,
msigdbr, org.Mm.eg.db, pheatmap, phytools, purrr, scales,
SummarizedExperiment, stringdist, tensorflow, vegan, testthat
(>= 3.0.0)
Alexander Yermanos [aut, cre],
Andreas Agrafiotis [ctb],
Raphael Kuhn [ctb],
Victor Kreiner [ctb],
Damiano Robbiani [ctb],
Josephine Yates [ctb],
Jiami Han [ctb],
Chrysa Papadopoulou [ctb],
Cédric Weber [ctb],
Danielle Shlesinger [ctb],
Raphael Dizerens [ctb]