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An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions

Bioconductor version: Release (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))


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:

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


biocViews Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, Normalization, Pathways, Preprocessing, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
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), ggplotify (>= 0.1.2), ggrepel (>= 0.9.2), gprofiler2 (>= 0.2.1), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4), plot3Drgl (>= 1.0.3), reshape2 (>= 1.4.4), S4Vectors(>= 0.36.2), stats (>= 4.2.2), SummarizedExperiment(>= 1.28.0), UpSetR (>= 1.4.0), utils (>= 4.2.2)
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Source Package MultiRNAflow_1.2.0.tar.gz
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