MultiRNAflow

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

Bioconductor version: 3.23 · Package version: 1.10.0

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.

Installation

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

BiocManager::install("MultiRNAflow")

Details

Maintainer	Rodolphe Loubaton <loubaton.rodolphe@gmail.com>
Author	Rodolphe Loubaton [aut, cre] (ORCID: <https://orcid.org/0000-0002-1442-7270>), Nicolas Champagnat [aut, ths] (ORCID: <https://orcid.org/0000-0002-5128-2357>), Laurent Vallat [aut, ths] (ORCID: <https://orcid.org/0000-0002-5226-7706>), Pierre Vallois [aut] (ORCID: <https://orcid.org/0000-0002-2123-0142>), Région Grand Est [fnd], Cancéropôle Est [fnd]
License	GPL-3 \| file LICENSE
URL	https://github.com/loubator/MultiRNAflow
Bug Reports	https://github.com/loubator/MultiRNAflow/issues
Downloads rank	203
Source branch	RELEASE_3_23
biocViews	Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, Normalization, Pathways, Preprocessing, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization

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Source package

Dependencies

Depends: Mfuzz (>= 2.64.0), R (>= 4.4)

Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.20.0), DESeq2 (>= 1.44.0), factoextra (>= 1.0.7), FactoMineR (>= 2.11), ggalluvial (>= 0.12.5), ggplot2 (>= 3.5.1), ggplotify (>= 0.1.2), ggrepel (>= 0.9.5), gprofiler2 (>= 0.2.3), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4.1), plot3Drgl (>= 1.0.4), reshape2 (>= 1.4.4), rlang (>= 1.1.6), S4Vectors (>= 0.42.0), stats (>= 4.2.2), SummarizedExperiment (>= 1.34.0), UpSetR (>= 1.4.0), utils (>= 4.2.2)

Suggests: BiocGenerics (>= 0.40.0), BiocStyle (>= 2.32.1), e1071 (>= 1.7.12), knitr (>= 1.47), rmarkdown (>= 2.27), testthat (>= 3.0.0)