RFLOMICS
This is the released version of RFLOMICS; for the devel version, see RFLOMICS.
Interactive web application for Omics-data analysis
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Metabolomics, Proteomics, ShinyApps, Software, Transcriptomics |
| Version | 1.4.2 |
| 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 |
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_1.4.2.tar.gz |
| Windows Binary (x86_64) | RFLOMICS_1.4.2.zip |
| macOS Binary (big-sur-x86_64) | RFLOMICS_1.4.2.tgz |
| macOS Binary (sonoma-arm64) | RFLOMICS_1.4.2.tgz |
| 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 |
| Old Source Packages for BioC 3.23 | Source Archive |