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biocLite("categoryCompare")
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categoryCompare
Meta-analysis of high-throughput experiments using feature annotations
Bioconductor version: 3.0
Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Author: Robert M. Flight <rflight79 at gmail.com>
Maintainer: Robert M. Flight <rflight79 at gmail.com>
Citation (from within R,
enter citation("categoryCompare")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("categoryCompare")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("categoryCompare")
| HTML | R Script | categoryCompare: High-throughput data meta-analysis using feature annotations |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, GO, GeneExpression, MultipleComparison, Pathways, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL-2 |
| Depends | R (>= 2.10), Biobase, BiocGenerics |
| Imports | AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape(>= 1.5.11) |
| LinkingTo | |
| Suggests | knitr, methods, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter |
| SystemRequirements | Cytoscape (>= 2.8.0) (if used for visualization of results, heavily suggested), CytoscapeRPC plugin (>= 1.8) |
| Enhances | |
| URL | https://github.com/rmflight/categoryCompare |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | categoryCompare_1.10.0.tar.gz |
| Windows Binary | categoryCompare_1.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | categoryCompare_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | categoryCompare_1.10.0.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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