DOI: 10.18129/B9.bioc.MultiRNAflow  

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

An R package for analysing RNA-seq raw counts with several biological conditions and different time points

Bioconductor version: Development (3.19)

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

Author: Rodolphe Loubaton [aut, cre] , Nicolas Champagnat [aut, ths] , Laurent Vallat [aut, ths] , Pierre Vallois [aut] , Région Grand Est [fnd], Cancéropôle Est [fnd]

Maintainer: Rodolphe Loubaton <loubaton.rodolphe at>

Citation (from within R, enter citation("MultiRNAflow")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script MultiRNAflow: A R package for analysing RNA-seq raw counts with different time points and several biological conditions.
HTML R Script Running_analysis_with_MultiRNAflow
PDF   Reference Manual
Text   NEWS


biocViews Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, Normalization, Pathways, Preprocessing, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization
Version 1.1.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3 | file LICENSE
Depends Mfuzz(>= 2.58.0), R (>= 4.3)
Imports Biobase(>= 2.54.0), ComplexHeatmap(>= 2.14.0), DESeq2(>= 1.38.1), factoextra (>= 1.0.7), FactoMineR (>= 2.6), ggalluvial (>= 0.12.3), ggplot2 (>= 3.4.0), ggrepel (>= 0.9.2), ggsci (>= 2.9), gprofiler2 (>= 0.2.1), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), methods (>= 4.2.2), plot3D (>= 1.4), plot3Drgl (>= 1.0.3), plyr (>= 1.8.8), RColorBrewer (>= 1.1.3), reshape2 (>= 1.4.4), rlang (>= 1.1.1), S4Vectors(>= 0.36.2), scales (>= 1.2.1), stats (>= 4.2.2), SummarizedExperiment(>= 1.28.0), UpSetR (>= 1.4.0), utils (>= 4.2.2)
Suggests BiocGenerics(>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0)
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MultiRNAflow_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64) MultiRNAflow_1.1.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: