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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SpidermiR")
In most cases, you don't need to download the package archive at all.
SpidermiR
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SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
Bioconductor version: Release (3.5)
The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miR2Disease,miRTar, miRTarBase, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).
Author: Claudia Cava, Antonio Colaprico, Alex Graudenzi, Gloria Bertoli, Tiago C. Silva, Catharina Olsen, Houtan Noushmehr, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni
Maintainer: Claudia Cava <claudia.cava at ibfm.cnr.it>
Citation (from within R,
enter citation("SpidermiR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SpidermiR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpidermiR")
| R Script | SpidermiR examples | |
| HTML | R Script | Working with SpidermiR package |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneRegulation, Network, Software, miRNA |
| Version | 1.7.4 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.0.0) |
| Imports | networkD3, httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots, grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks, gdata |
| LinkingTo | |
| Suggests | BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/claudiacava/SpidermiR |
| BugReports | https://github.com/claudiacava/SpidermiR/issues |
| Depends On Me | |
| Imports Me | StarBioTrek |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SpidermiR_1.7.4.tar.gz |
| Windows Binary | SpidermiR_1.7.4.zip |
| Mac OS X 10.11 (El Capitan) | SpidermiR_1.7.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpidermiR |
| Package Short Url | http://bioconductor.org/packages/SpidermiR/ |
| Package Downloads Report | Download Stats |
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