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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("KEGGprofile")
In most cases, you don't need to download the package archive at all.
KEGGprofile
An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
Bioconductor version: 3.0
KEGGprofile is an annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. KEGGprofile facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples.
Author: Shilin Zhao, Yu Shyr
Maintainer: Shilin Zhao <shilin.zhao at vanderbilt.edu>
Citation (from within R,
enter citation("KEGGprofile")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("KEGGprofile")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("KEGGprofile")
| R Script | KEGGprofile: Application Examples | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Pathways, Software |
| Version | 1.8.2 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | GPL (>= 2) |
| Depends | |
| Imports | AnnotationDbi, png, TeachingDemos, XML, KEGG.db, KEGGREST, biomaRt |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | FGNet |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | KEGGprofile_1.8.2.tar.gz |
| Windows Binary | KEGGprofile_1.8.2.zip |
| Mac OS X 10.6 (Snow Leopard) | KEGGprofile_1.8.2.tgz |
| Mac OS X 10.9 (Mavericks) | KEGGprofile_1.8.2.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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