DOI: 10.18129/B9.bioc.SpidermiR    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SpidermiR.

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

Bioconductor version: 3.15

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, miRTarBase, miRandola, Miranda, PicTar and TargetScan). Furthermore, we also present a statistical test to identify pharmaco-mir relationships using the gene-drug interactions derived by DGIdb and MATADOR database.

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 1.26.1
In Bioconductor since BioC 3.3 (R-3.3) (6.5 years)
License GPL (>= 3)
Depends R (>= 3.0.0)
Imports httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, 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
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Source Package SpidermiR_1.26.1.tar.gz
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