MultiRNAflow

DOI: 10.18129/B9.bioc.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>

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")

 

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
Text		LICENSE

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)
LinkingTo
Suggests	BiocGenerics(>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/loubator/MultiRNAflow
BugReports	https://github.com/loubator/MultiRNAflow/issues
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_1.0.0.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
Old Source Packages for BioC 3.18	Source Archive