To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("geecc")
In most cases, you don't need to download the package archive at all.
geecc
Gene set Enrichment analysis Extended to Contingency Cubes
Bioconductor version: 3.0
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, chromosmal position, phylostrata, ....
Author: Markus Boenn
Maintainer: Markus Boenn <markus.boenn at ufz.de>
Citation (from within R,
enter citation("geecc")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("geecc")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("geecc")
| R Script | geecc User's Guide | |
| Reference Manual |
Details
| biocViews | BiologicalQuestion, GO, GeneExpression, GeneSetEnrichment, Microarray, RNASeq, Software, StatisticalMethod, Transcription, WorkflowStep |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.0), methods |
| Imports | MASS, hypergea (>= 1.2.3), gplots |
| LinkingTo | |
| Suggests | hgu133plus2.db, GO.db, AnnotationDbi |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | geecc_1.0.0.tar.gz |
| Windows Binary | geecc_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | geecc_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | geecc_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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