InterMineR

DOI: 10.18129/B9.bioc.InterMineR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see InterMineR.

R Interface with InterMine-Powered Databases

Bioconductor version: 3.8

Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. This R package provides interfaces with these databases through webservices. It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.

Author: Bing Wang, Julie Sullivan, Rachel Lyne, Konstantinos Kyritsis

Maintainer: InterMine Team <j.sullivan at gen.cam.ac.uk>

Installation

To install this package, start R (version "3.5") and enter:

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

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("InterMineR")

 

HTML	R Script	Enrichment Analysis and Visualization
HTML	R Script	FlyMine Genomic Visualizations
HTML	R Script	InterMineR Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, ComparativeGenomics, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, GenomeWideAssociation, KEGG, Microarray, MultipleComparison, Pathways, Proteomics, Reactome, SNP, Software, SystemsBiology, Visualization
Version	1.4.1
In Bioconductor since	BioC 3.6 (R-3.4) (1.5 years)
License	LGPL
Depends	R (>= 3.4.1)
Imports	Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods
LinkingTo
Suggests	BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db
SystemRequirements
Enhances
URL
BugReports	https://github.com/intermine/intermineR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	InterMineR_1.4.1.tar.gz
Windows Binary	InterMineR_1.4.1.zip
Mac OS X 10.11 (El Capitan)	InterMineR_1.4.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InterMineR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/InterMineR
Package Short Url	http://bioconductor.org/packages/InterMineR/
Package Downloads Report	Download Stats