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DESCRIPTION
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DESCRIPTION
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Package: DspikeIn
Type: Package
Title: Quantifying Absolute Abundance to Enhance Microbial Dynamics Assessment
Version: 0.0.0.9000
Author: Mitra Ghotbi
Maintainer: Mitra Ghotbi <[email protected]>
Description: The DspikeIn package enables the quantification of absolute microbial abundance, improving the evaluation of microbial dynamics — a critical aspect in microbial ecology research. It extends the functionality of the phyloseq package and integrates enhanced or modified functions from several key packages, including dplyr, stats, ggplot2, edgeR, ggtree, flextable, DESeq2, microbiomeutilities, DECIPHER, and speedyseq.
Acknowledgements: DspikeIn is built upon the phyloseq package and utilizes additional functionality from dplyr, ggtree, flextable, DESeq2, edgeR, microbiomeutilities, DECIPHER, and speedyseq, among others.
URL: https://github.com/mghotbi/DspikeIn
BugReports: https://github.com/mghotbi/DspikeIn/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
R (>= 3.5.0)
Imports:
tibble,
limma,
phyloseq,
msa,
stats,
DESeq2,
edgeR,
dplyr,
ggplot2,
ggtree,
flextable,
Biostrings,
DECIPHER,
randomForest,
ggridges,
phangorn,
ggalluvial,
microbiome,
matrixStats,
RColorBrewer,
ape,
rlang,
scales,
magrittr,
ggpubr,
microbiomeutilities,
speedyseq,
methods
Remotes:
mikemc/speedyseq,
microsud/microbiomeutilities
Suggests:
ShortRead,
agricolae,
testthat (>= 3.0.0),
devtools,
dada2,
BiocManager,
DT,
data.table,
preprocessCore,
Biobase,
e1071,
caret,
qpdf,
optparse,
foreach,
viridis,
plyr,
reshape2,
grid,
cluster,
intergraph,
ggtext,
remotes
RoxygenNote: 7.3.1.9000
Packaged: 2024-07-28 21:21:56 UTC; mghotbi
NeedsCompilation: no