RFLOMICS

This is the released version of RFLOMICS; for the devel version, see RFLOMICS.

Interactive web application for Omics-data analysis

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DOI: 10.18129/B9.bioc.RFLOMICS

Bioconductor version: Release (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 iD ORCID: 0000-0001-6931-2529 , Delphine Charif [aut] ORCID iD ORCID: 0000-0002-1949-5969 , Audrey Hulot [aut] ORCID iD ORCID: 0000-0002-9647-6470 , Christine Paysant-Leroux [aut] ORCID iD 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")
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")

RFLOMICS HTML R Script

RFLOMICS Command line HTML R Script

RFLOMICS input format HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, Metabolomics, Proteomics, ShinyApps, Software, Transcriptomics

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License Artistic-2.0

Depends R (>= 4.4.0), SummarizedExperiment, MultiAssayExperiment, shinyBS, dplyr, ggplot2, htmltools, knitr, coseq

Imports vroom, org.At.tair.db, AnnotationDbi, clusterProfiler, ComplexHeatmap, data.table, DT, edgeR, enrichplot, FactoMineR, ggpubr, ggrepel, grDevices, grid, httr, limma, magrittr, methods, mixOmics, MOFA2, plotly, 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

Suggests testthat, shinytest2, BiocStyle, org.Hs.eg.db

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Package Archives

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

Source Package RFLOMICS_1.2.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) RFLOMICS_1.2.0.tgz

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/RFLOMICS

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RFLOMICS

Bioc Package Browser https://code.bioconductor.org/browse/RFLOMICS/

Package Short Url https://bioconductor.org/packages/RFLOMICS/

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