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InterMineR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

R Interface with InterMine-Powered Databases


Bioconductor version: Development (3.19)

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, Celia Sanchez

Maintainer: InterMine Team <r.lyne at gen.cam.ac.uk>

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

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("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")
InterMineR Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, ComparativeGenomics, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GeneRegulation, GeneSetEnrichment, GenomeAnnotation, GenomeWideAssociation, KEGG, Microarray, MultipleComparison, Pathways, Proteomics, Reactome, SNP, Software, SystemsBiology, Visualization
Version 1.25.1
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License LGPL
Depends R (>= 3.4.1)
Imports Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods
System Requirements
URL
Bug Reports https://github.com/intermine/intermineR/issues
See More
Suggests BiocStyle, Gviz, knitr, rmarkdown, GO.db, org.Hs.eg.db
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 InterMineR_1.25.1.tar.gz
Windows Binary InterMineR_1.25.1.zip
macOS Binary (x86_64) InterMineR_1.25.1.tgz
macOS Binary (arm64)
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 https://bioconductor.org/packages/InterMineR/
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