RFLOMICS

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

Interactive web application for Omics-data analysis

Bioconductor version: Development (3.24)

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")):

Nadia Bessoltane, Delphine Charif, Audrey Hulot, Christine Paysant-Leroux, Gwendal Cueff. RFLOMICS: Interactive web application for Omics-data analysis. doi:10.18129/B9.bioc.RFLOMICS, R package version 1.5.0, https://bioconductor.org/packages/RFLOMICS.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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 Command line	HTML	R Script
RFLOMICS input format	HTML	R Script
RFLOMICS	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	1.5.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 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, FactoMineR, ggpubr, ggnetwork, 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RFLOMICS_1.5.0.tar.gz
Windows Binary (x86_64)	RFLOMICS_1.5.0.zip
macOS Binary (big-sur-x86_64)	RFLOMICS_1.5.0.tgz
macOS Binary (sonoma-arm64)	RFLOMICS_1.5.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RFLOMICS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RFLOMICS
Package Short Url	https://bioconductor.org/packages/RFLOMICS/
Package Downloads Report	Download Stats