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 package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see InterMineR.
R Interface with InterMine-Powered Databases
Bioconductor version: Release (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("InterMineR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| InterMineR Vignette | HTML | R Script |
| Reference Manual | ||
| 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 | 1.26.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | InterMineR_1.26.0.zip |
| macOS Binary (x86_64) | InterMineR_1.26.0.tgz |
| macOS Binary (arm64) | InterMineR_1.26.0.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 | https://bioconductor.org/packages/InterMineR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |