This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see TimiRGeN.

Time sensitive microRNA-mRNA integration, analysis and network generation tool

Bioconductor version: 3.18

TimiRGeN (Time Incorporated miR-mRNA Generation of Networks) is a novel R package which functionally analyses and integrates time course miRNA-mRNA differential expression data. This tool can generate small networks within R or export results into cytoscape or pathvisio for more detailed network construction and hypothesis generation. This tool is created for researchers that wish to dive deep into time series multi-omic datasets. TimiRGeN goes further than many other tools in terms of data reduction. Here, potentially hundreds-of-thousands of potential miRNA-mRNA interactions can be whittled down into a handful of high confidence miRNA-mRNA interactions affecting a signalling pathway, across a time course.

Author: Krutik Patel [aut, cre]

Maintainer: Krutik Patel <krutik.patel at newcastle.ac.uk>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

TimiRGeN HTML R Script
Reference Manual PDF


biocViews Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.1), Mfuzz, MultiAssayExperiment
Imports biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools (>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics, grDevices, igraph (>=, RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0)
System Requirements
URL https://github.com/Krutik6/TimiRGeN/
Bug Reports https://github.com/Krutik6/TimiRGeN/issues
See More
Suggests BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package TimiRGeN_1.11.0.tar.gz
Windows Binary TimiRGeN_1.11.0.zip
macOS Binary (x86_64) TimiRGeN_1.11.0.tgz
macOS Binary (arm64) TimiRGeN_1.11.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TimiRGeN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TimiRGeN
Bioc Package Browser https://code.bioconductor.org/browse/TimiRGeN/
Package Short Url https://bioconductor.org/packages/TimiRGeN/
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