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RFLOMICS

This is the development version of RFLOMICS; to use it, please install the devel version of Bioconductor.

Interactive web application for Omics-data analysis


Bioconductor version: Development (3.21)

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")

# 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")
RFLOMICS HTML R Script
RFLOMICS Command line HTML R Script
RFLOMICS input format HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Metabolomics, Proteomics, ShinyApps, Software, Transcriptomics
Version 0.99.7
In Bioconductor since BioC 3.21 (R-4.5)
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
URL https://github.com/RFLOMICS/RFLOMICS
Bug Reports https://github.com/RFLOMICS/RFLOMICS/issues
See More
Suggests testthat, shinytest2, BiocStyle, org.Hs.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package RFLOMICS_0.99.7.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64) RFLOMICS_0.99.7.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/
Package Downloads Report Download Stats