IntramiRExploreR

Predicting Targets for Drosophila Intragenic miRNAs

Bioconductor version: Release (3.17)

Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.

Author: Surajit Bhattacharya and Daniel Cox

Maintainer: Surajit Bhattacharya <sbhattach2 at childrensnational.org>

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("IntramiRExploreR")

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("IntramiRExploreR")

IntramiRExploreR	HTML	R Script
IntramiRExploreR.pdf	PDF
Reference Manual	PDF

Details

biocViews	GeneExpression, GenePrediction, GeneTarget, Microarray, Software, StatisticalMethod
Version	1.22.0
In Bioconductor since	BioC 3.6 (R-3.4) (6 years)
License	GPL-2
Depends	R (>= 3.4)
Imports	igraph (>= 1.0.1), FGNet(>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics
Linking To
Suggests	gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
System Requirements
Enhances
URL	https://github.com/VilainLab/IntramiRExploreR
Bug Reports	https://github.com/VilainLab/IntramiRExploreR

Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	IntramiRExploreR_1.22.0.tar.gz
Windows Binary	IntramiRExploreR_1.22.0.zip
macOS Binary (x86_64)	IntramiRExploreR_1.22.0.tgz
macOS Binary (arm64)	IntramiRExploreR_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IntramiRExploreR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IntramiRExploreR
Bioc Package Browser	https://code.bioconductor.org/browse/IntramiRExploreR/
Package Short Url	https://bioconductor.org/packages/IntramiRExploreR/
Package Downloads Report	Download Stats