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Bioconductor - RFLOMICS (development version)

RFLOMICS

This is the development version of RFLOMICS; for the stable release version, see RFLOMICS.

Interactive web application for Omics-data analysis

Bioconductor version: Development (3.22)

R-package with shiny interface, provides a framework for the analysis of transcriptomics, proteomics and/or metabolomics data. The interface offers a guided experience for the user, from the definition of the experimental design to the integration of several omics table together. A report can be generated with all settings and analysis results.

Author: Nadia Bessoltane [aut, cre] ORCID: 0000-0001-6931-2529 , Delphine Charif [aut] ORCID: 0000-0002-1949-5969 , Audrey Hulot [aut] ORCID: 0000-0002-9647-6470 , Christine Paysant-Leroux [aut] ORCID: 0000-0003-2046-6492 , Gwendal Cueff [aut]

Maintainer: Nadia Bessoltane <nadia.bessoltane at inrae.fr>

Citation (from within R, enter citation("RFLOMICS")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RFLOMICS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RFLOMICS")

Details biocViews DifferentialExpression, Metabolomics, Proteomics, ShinyApps, Software, Transcriptomics Version 1.1.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) License Artistic-2.0 Depends R (>= 4.4.0), SummarizedExperiment, MultiAssayExperiment, shinyBS, dplyr, ggplot2, htmltools, knitr, coseq Imports vroom, org.At.tair.db, AnnotationDbi, circlize, clusterProfiler, ComplexHeatmap, data.table, DT, edgeR, EnhancedVolcano, enrichplot, FactoMineR, ggpubr, ggrepel, grDevices, grid, httr, limma, magrittr, methods, mixOmics, MOFA2, purrr, RColorBrewer, reshape2, reticulate, rmarkdown, S4Vectors, shiny, shinydashboard, shinyWidgets, stats, stringr, tidyr, tibble, tidyselect, UpSetR System Requirements Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2 (>=0.7.1) URL https://github.com/RFLOMICS/RFLOMICS Bug Reports https://github.com/RFLOMICS/RFLOMICS/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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