SpidermiR

DOI: 10.18129/B9.bioc.SpidermiR    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("SpidermiR")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SpidermiR")

 

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

Details

biocViews	GeneRegulation, Network, Software, miRNA
Version	1.22.1
In Bioconductor since	BioC 3.3 (R-3.3) (5.5 years)
License	GPL (>= 3)
Depends	R (>= 3.0.0)
Imports	httr, igraph, utils, stats, miRNAtap, miRNAtap.db, AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots, grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks, gdata, MAGeCKFlute, networkD3
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
Links To Me
Build Report

Package Archives

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

Source Package	SpidermiR_1.22.1.tar.gz
Windows Binary	SpidermiR_1.22.1.zip
macOS 10.13 (High Sierra)	SpidermiR_1.22.1.tgz
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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive