geecc
This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see geecc.
Gene Set Enrichment Analysis Extended to Contingency Cubes
Bioconductor version: 3.11
Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosomal position, phylostrata, divergence-strata, ....
Author: Markus Boenn
Maintainer: Markus Boenn <markus.boenn at ufz.de>
citation("geecc")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("geecc")
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("geecc")| geecc User's Guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, Microarray, RNASeq, Software, StatisticalMethod, Transcription, WorkflowStep |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.3.0), methods |
| Imports | MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils |
| System Requirements | Rcpp |
| URL |
See More
| Suggests | hgu133plus2.db, GO.db, AnnotationDbi |
| Linking To | Rcpp |
| 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 | geecc_1.21.0.tar.gz |
| Windows Binary | geecc_1.21.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/geecc |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/geecc |
| Bioc Package Browser | https://code.bioconductor.org/browse/geecc/ |
| Package Short Url | https://bioconductor.org/packages/geecc/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |