IntramiRExploreR
This is the released version of IntramiRExploreR; for the devel version, see IntramiRExploreR.
Predicting Targets for Drosophila Intragenic miRNAs
Bioconductor version: Release (3.23)
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("IntramiRExploreR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| Reference Manual |
Details
| biocViews | GeneExpression, GenePrediction, GeneTarget, Microarray, Software, StatisticalMethod |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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 |
| System Requirements | |
| URL | https://github.com/VilainLab/IntramiRExploreR |
| Bug Reports | https://github.com/VilainLab/IntramiRExploreR |
See More
| Suggests | gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IntramiRExploreR_1.34.0.tar.gz |
| Windows Binary (x86_64) | IntramiRExploreR_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | IntramiRExploreR_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | IntramiRExploreR_1.34.0.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 |