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MultiRNAflow

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


Bioconductor version: Release (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


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

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 1.0.0
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)
System Requirements
URL https://github.com/loubator/MultiRNAflow
Bug Reports https://github.com/loubator/MultiRNAflow/issues
See More
Suggests BiocGenerics(>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

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

Source Package MultiRNAflow_1.0.0.tar.gz
Windows Binary MultiRNAflow_1.0.0.zip
macOS Binary (x86_64) MultiRNAflow_1.0.0.tgz
macOS Binary (arm64) MultiRNAflow_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MultiRNAflow
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MultiRNAflow
Bioc Package Browser https://code.bioconductor.org/browse/MultiRNAflow/
Package Short Url https://bioconductor.org/packages/MultiRNAflow/
Package Downloads Report Download Stats