RFLOMICS

Interactive web application for Omics-data analysis

Bioconductor version: 3.23 · Package version: 1.4.2

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.

Installation

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

BiocManager::install("RFLOMICS")

Details

Maintainer	Nadia Bessoltane <nadia.bessoltane@inrae.fr>
Author	Nadia Bessoltane [aut, cre] (ORCID: <https://orcid.org/0000-0001-6931-2529>), Delphine Charif [aut] (ORCID: <https://orcid.org/0000-0002-1949-5969>), Audrey Hulot [aut] (ORCID: <https://orcid.org/0000-0002-9647-6470>), Christine Paysant-Leroux [aut] (ORCID: <https://orcid.org/0000-0003-2046-6492>), Gwendal Cueff [aut]
License	Artistic-2.0
URL	https://github.com/RFLOMICS/RFLOMICS
Bug Reports	https://github.com/RFLOMICS/RFLOMICS/issues
System Requirements	Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2 (>=0.7.1)
Downloads rank	167
Source branch	RELEASE_3_23
biocViews	DifferentialExpression, Metabolomics, Proteomics, ShinyApps, Software, Transcriptomics

Documentation

Download

Source package

Dependencies

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

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