TimiRGeN
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see TimiRGeN.
Time sensitive microRNA-mRNA integration, analysis and network generation tool
Bioconductor version: 3.15
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>
citation("TimiRGeN")):
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")| TimiRGeN | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, Network, Pathways, Software, TimeCourse, Visualization, miRNA |
| Version | 1.6.0 |
| 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 (>= 1.2.4.2), 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/TimiRGeN/ |
| Package Short Url | https://bioconductor.org/packages/TimiRGeN/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |