MultiRNAflow
An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
Bioconductor version: 3.24 · Package version: 1.11.0
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 | 386 |
| Source branch | devel |
| biocViews | Clustering, DifferentialExpression, GeneExpression, GeneSetEnrichment, Normalization, Pathways, Preprocessing, PrincipalComponent, RNASeq, Sequencing, Software, TimeCourse, Transcription, Visualization |
Documentation
- MultiRNAflow: A R package for analysing RNA-seq raw counts with different time points and several biological conditions.
- Running MultiRNAflow on a RNA-seq raw counts with different time points and several biological conditions
Download
Follow the installation instructions to use this package in your R session.
| Source package | MultiRNAflow_1.11.0.tar.gz |
| Windows binary (x86_64) | MultiRNAflow_1.11.0.zip |
| macOS binary (arm64) | MultiRNAflow_1.11.0.tgz |
| macOS binary (x86_64) | MultiRNAflow_1.11.0.tgz |
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)