Imports: caret, DT, foreach, ggplot2, heatmaply, matrixStats, plotly,
plyr, pROC, purrr, shiny, shinycssloaders, shinyFiles,
shinydashboard, shinyjs, shinyWidgets, stats, survival,
Suggests: testthat (>= 3.0.0), ggfortify, knitr, rmarkdown
Packaged: 2022-05-18 13:58:40 UTC; danielebizzarri

pROC, purrr, shiny, shinycssloaders, shinyFiles,
Packaged: 2022-05-23 09:11:13 UTC; danielebizzarri

Title: Adaptive Normalization for miRNA Data
person("Yuda", "Zhu", email = "yudazhu@gmail.com", role = c("aut", "cre")),
person("Amanda", "Zhao", email = "happysundae@gmail.com", role = c("aut")))
Description: An adaptive normalization algorithm that selects housekeeping genes
based on the sample level variability in the data. This is suitable for any data
obtained from RT-qPCR assays.  A manuscript describing the method is submitted
to Genome Biology under ``MiRA-norm: An Adaptive Method for the Normalization of MicroRNA Array Data``, Yuda Zhu et al.
Imports: grDevices, graphics, stats, utils, ggplot2, cluster, npmv,
dendextend, parallel, MASS, plyr, reshape2, ArgumentCheck

Title: Microbiome Regression-Based Kernel Association Test
Authors@R: c(person("Haotian", "Zheng", role = c("aut"),
person("Anna", "Plantinga", role = "aut"),
person("Ni", "Zhao", role = c("aut", "cre"), email = "nzhao10@jhu.edu"),
Depends: R (>= 2.13.0), survival, PearsonDS, GUniFrac, MASS
Description: Test for overall association between microbiome composition data with a continuous or dichotomous outcome via phylogenetic kernels. The phenotype can be univariate continuous or binary phenotypes (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). For all these effect, the microbiome community effect was modeled nonparametrically through a kernel function, which can incorporate the phylogenetic tree information.

person("Ni", "Zhao", role = c("aut", "cre"), email = "nzhao10@jhu.edu"))
Author: Haotian Zheng [aut], Xiang Zhan [aut], Anna Plantinga [aut], Michael Wu [aut], Ni Zhao [aut, cre]