DOI: 10.18129/B9.bioc.SpidermiR    

SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data

Bioconductor version: Release (3.6)

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>

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biocViews GeneRegulation, Network, Software, miRNA
Version 1.8.2
In Bioconductor since BioC 3.3 (R-3.3) (2 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
Suggests BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
URL https://github.com/claudiacava/SpidermiR
BugReports https://github.com/claudiacava/SpidermiR/issues
Depends On Me
Imports Me StarBioTrek
Suggests Me
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Source Package SpidermiR_1.8.2.tar.gz
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Mac OS X 10.11 (El Capitan) SpidermiR_1.8.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/SpidermiR
Package Short Url http://bioconductor.org/packages/SpidermiR/
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