To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CAFE")
In most cases, you don't need to download the package archive at all.
CAFE
Chromosmal Aberrations Finder in Expression data
Bioconductor version: 3.0
Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input
Author: Sander Bollen
Maintainer: Sander Bollen <sander.h.bollen at gmail.com>
Citation (from within R,
enter citation("CAFE")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CAFE")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CAFE")
| R Script | Manual | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Microarray, OneChannel, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio |
| Imports | affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, BiocStyle |
| 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 | CAFE_1.2.0.tar.gz |
| Windows Binary | CAFE_1.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | CAFE_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | CAFE_1.2.0.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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