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Bioconductor - MultiRNAflow (development version)

MultiRNAflow

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

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

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-1442-7270 , Nicolas Champagnat [aut, ths] ORCID: 0000-0002-5128-2357 , Laurent Vallat [aut, ths] ORCID: 0000-0002-5226-7706 , Pierre Vallois [aut] ORCID: 0000-0002-2123-0142 , Région Grand Est [fnd], Cancéropôle Est [fnd]

Maintainer: Rodolphe Loubaton <loubaton.rodolphe at gmail.com>

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

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("MultiRNAflow")
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 NEWS Text LICENSE Text Details biocViews Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, Normalization, Pathways, Preprocessing, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization Version 1.7.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 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) System Requirements URL https://github.com/loubator/MultiRNAflow Bug Reports https://github.com/loubator/MultiRNAflow/issues See More Package Archives

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

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