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SpidermiR

This is the development version of SpidermiR; for the stable release version, see SpidermiR.

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


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SpidermiR")

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

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews GeneRegulation, Network, Software, miRNA
Version 1.33.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
Linking To
Enhances
Depends On Me
Imports Me StarBioTrek
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SpidermiR_1.33.0.tar.gz
Windows Binary SpidermiR_1.33.0.zip
macOS Binary (x86_64) SpidermiR_1.33.0.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/SpidermiR/
Package Short Url https://bioconductor.org/packages/SpidermiR/
Package Downloads Report Download Stats