SpidermiR
This package is for version 3.11 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: 3.11
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("SpidermiR")):
Installation
To install this package, start R (version "4.0") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpidermiR")| Working with SpidermiR package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, Network, Software, miRNA |
| Version | 1.18.2 |
| 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, ggplot2, gridExtra, gplots, grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks, gdata, MAGeCKFlute, networkD3 |
| 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_1.18.2.tar.gz |
| Windows Binary | SpidermiR_1.18.2.zip |
| macOS 10.13 (High Sierra) | SpidermiR_1.18.2.tgz |
| 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 |
| Old Source Packages for BioC 3.11 | Source Archive |