To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("gaga")
In most cases, you don't need to download the package archive at all.
gaga
GaGa hierarchical model for high-throughput data analysis
Bioconductor version: 3.0
Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).
Author: David Rossell <rosselldavid at gmail.com>.
Maintainer: David Rossell <rosselldavid at gmail.com>
Citation (from within R,
enter citation("gaga")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("gaga")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gaga")
| R Script | Manual for the gaga library | |
| Reference Manual |
Details
| biocViews | Classification, DifferentialExpression, MassSpectrometry, MultipleComparison, OneChannel, Software |
| Version | 2.12.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) |
| License | GPL (>= 2) |
| Depends | R (>= 2.8.0), Biobase, coda, EBarrays, mgcv |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | |
| Imports Me | casper |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | gaga_2.12.0.tar.gz |
| Windows Binary | gaga_2.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | gaga_2.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | gaga_2.12.0.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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