SpidermiR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SpidermiR.

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


Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("SpidermiR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpidermiR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneRegulation, Network, Software, miRNA
Version 1.34.0
In Bioconductor since BioC 3.3 (R-3.3) (8.5 years)
License GPL (>= 3)
Depends R (>= 3.0.0)
Imports httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, gdata
System Requirements
URL https://github.com/claudiacava/SpidermiR
Bug Reports https://github.com/claudiacava/SpidermiR/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SpidermiR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpidermiR
Package Short Url https://bioconductor.org/packages/SpidermiR/
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