TimiRGeN

DOI: 10.18129/B9.bioc.TimiRGeN    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TimiRGeN")

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("TimiRGeN")

 

HTML	R Script	TimiRGeN
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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 (>= 1.2.4.2), RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0)
LinkingTo
Suggests	BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/Krutik6/TimiRGeN/
BugReports	https://github.com/Krutik6/TimiRGeN/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	TimiRGeN_1.6.0.tar.gz
Windows Binary	TimiRGeN_1.6.0.zip
macOS Binary (x86_64)	TimiRGeN_1.6.0.tgz
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
Old Source Packages for BioC 3.15	Source Archive