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DESCRIPTION
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DESCRIPTION
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Package: MicrobiomeAnalysis
Type: Package
Title: Data analysis toolkits in metagenomics
Version: 1.0.3
Date: 2022-05-14
Authors@R:
person(given = "Hua",
family = "Zou",
role = c("cre", "aut"),
email = "[email protected]")
Description: MicrobiomeAnalysis is an R package for analysis and visualization.
It converts the inputs into phyloseq or ExpressionSet class. In addition,
it separates the data analysis and visualization into two parts.
License: GPL (>= 3.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
ByteCompile: true
biocViews: Metagenomics, DifferentialAnalysis, FeatureSelection, Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
URL: https://github.com/HuaZou/MicrobiomeAnalysis
BugReports: https://github.com/HuaZou/MicrobiomeAnalysis/issues
Depends:
R (>= 4.1.0)
Imports:
dplyr,
phyloseq,
magrittr,
purrr,
MASS,
utils,
ggplot2,
tibble,
rlang,
stats,
coin,
methods,
IRanges,
tidyr,
metagenomeSeq,
DESeq2,
edgeR,
BiocGenerics,
Biostrings,
yaml,
biomformat,
S4Vectors,
Biobase,
ComplexHeatmap,
ANCOMBC,
caret,
limma,
ALDEx2,
multtest,
plotROC,
vegan,
RColorBrewer,
SummarizedExperiment
Suggests:
testthat,
rmarkdown,
knitr,
ape,
permute,
ade4,
geosphere,
compositions,
ggtree,
tidytree,
patchwork,
ggsignif,
imputeLCMD,
missForest,
ape,
Rtsne,
umap,
impute,
ropls