InterMineR
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see InterMineR.
R Interface with InterMine-Powered Databases
Bioconductor version: 3.7
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>
citation("InterMineR")):
Installation
To install this package, start R (version "3.5") 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")| Enrichment Analysis and Visualization | HTML | R Script |
| FlyMine Genomic Visualizations | HTML | R Script |
| 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 | 1.2.1 |
| 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, GeneAnswers, 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_1.2.1.tar.gz |
| Windows Binary | InterMineR_1.2.1.zip |
| Mac OS X 10.11 (El Capitan) | InterMineR_1.2.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/InterMineR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/InterMineR |
| Bioc Package Browser | https://code.bioconductor.org/browse/InterMineR/ |
| Package Short Url | https://bioconductor.org/packages/InterMineR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |