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

 

   

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")

 

PDF R Script SpidermiR examples
HTML R Script Working with SpidermiR package
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Network, Software, miRNA
Version 1.6.2
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
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.

Package Source SpidermiR_1.6.2.tar.gz
Windows Binary SpidermiR_1.6.2.zip
Mac OS X 10.11 (El Capitan) SpidermiR_1.6.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SpidermiR/tree/release-3.5
Package Short Url http://bioconductor.org/packages/SpidermiR/
Package Downloads Report Download Stats

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