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]
, Delphine Charif [aut]
, Audrey Hulot [aut]
, Christine Paysant-Leroux [aut]
, Gwendal Cueff [aut]
Maintainer: Nadia Bessoltane <nadia.bessoltane at inrae.fr>
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 | ||
| NEWS | Text |
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
| 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_1.1.0.tar.gz |
| Windows Binary (x86_64) | RFLOMICS_1.1.0.zip |
| macOS Binary (x86_64) | RFLOMICS_1.1.0.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/ |
| Package Downloads Report | Download Stats |