MultiRNAflow
An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
Bioconductor version: Release (3.20)
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("MultiRNAflow")):
Installation
To install this package, start R (version "4.4") 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. | R Script | |
| Running_analysis_with_MultiRNAflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, Normalization, Pathways, Preprocessing, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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
| Suggests | BiocGenerics(>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MultiRNAflow_1.4.0.tar.gz |
| Windows Binary (x86_64) | MultiRNAflow_1.4.0.zip |
| macOS Binary (x86_64) | MultiRNAflow_1.4.0.tgz |
| macOS Binary (arm64) | MultiRNAflow_1.4.0.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 |