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DESCRIPTION
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Package: phenomis
Type: Package
Title: Postprocessing and univariate analysis of omics data
Version: 0.99.16
Date: 2022-08-26
Authors@R: c(
person(given = "Etienne A.", family = "Thevenot",
email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-1019-4577")),
person(given = "Natacha", family = "Lenuzza",
email = "[email protected]",
role = "ctb"),
person(given = "Alyssa", family = "Imbert",
email = "[email protected]",
role = "ctb"),
person(given = "Pierrick", family = "Roger",
email = "[email protected]",
role = "ctb"),
person(given = "Eric", family = "Venot",
email = "[email protected]",
role = "ctb"),
person(given = "Sylvain", family = "Dechaumet",
email = "[email protected]",
role = "ctb")
)
Description: The 'phenomis' package provides methods to perform post-processing
(i.e. quality control and normalization) as well as univariate statistical
analysis of single and multi-omics data sets. These methods include quality
control metrics, signal drift and batch effect correction, intensity
transformation, univariate hypothesis testing, but also clustering
(as well as annotation of metabolomics data). The data are handled in the
standard Bioconductor formats (i.e. SummarizedExperiment and
MultiAssayExperiment for single and multi-omics datasets, respectively; the
alternative ExpressionSet and MultiDataSet formats are also supported for
convenience). As a result, all methods can be readily chained as workflows.
The pipeline can be further enriched by multivariate analysis and feature
selection, by using the 'ropls' and 'biosigner' packages, which support
the same formats. Data can be conveniently imported from and exported to
text files. Although the methods were initially targeted to metabolomics
data, most of the methods can be applied to other types of omics data (e.g.,
transcriptomics, proteomics).
biocViews:
BatchEffect, Clustering, Coverage, KEGG, MassSpectrometry, Metabolomics,
Normalization, Proteomics, QualityControl, Sequencing, StatisticalMethod,
Transcriptomics
Depends:
SummarizedExperiment
Imports:
Biobase,
biodb,
biodbChebi,
data.table,
futile.logger,
ggplot2,
ggrepel,
graphics,
grDevices,
grid,
htmlwidgets,
igraph,
limma,
methods,
MultiAssayExperiment,
MultiDataSet,
PMCMRplus,
plotly,
ranger,
RColorBrewer,
ropls,
stats,
tibble,
tidyr,
utils,
VennDiagram
Suggests:
BiocGenerics,
BiocStyle,
biosigner,
CLL,
knitr,
omicade4,
rmarkdown,
testthat
VignetteBuilder: knitr
License: CeCILL
Encoding: UTF-8
LazyLoad: yes
URL: https://doi.org/10.1038/s41597-021-01095-3
RoxygenNote: 7.2.0