DOI: 10.18129/B9.bioc.TimiRGeN  

This is the development version of TimiRGeN; for the stable release version, see TimiRGeN.

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

Bioconductor version: Development (3.19)

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 <nkp68 at newcastle.ac.uk>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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


PDF   Reference Manual


biocViews Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version 1.13.1
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.3), 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)
Suggests BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown
URL https://github.com/Krutik6/TimiRGeN/
BugReports https://github.com/Krutik6/TimiRGeN/issues
Depends On Me
Imports Me
Suggests Me updateObject
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/TimiRGeN
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TimiRGeN
Package Short Url https://bioconductor.org/packages/TimiRGeN/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: