DOI: 10.18129/B9.bioc.TimiRGeN  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TimiRGeN.

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

Bioconductor version: 3.16

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>

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biocViews Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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)
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
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Source Package TimiRGeN_1.8.0.tar.gz
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