R Development Page
Contributed R Packages
Below is a list of all packages provided by project GADA.
Important note for package binaries: R-Forge provides these binaries only for the most recent version of R, but not for older versions. In order to successfully install the packages provided on R-Forge, you have to switch to the most recent version of R or, alternatively, install from the package sources (.tar.gz).
Packages
| gada | Genome Alteration Detection Algorithm (GADA) | |||||||||
| The package implements a flexible and efficient analysis pipeline to detect genomic copy number alterations from microarray data. It can import the raw copy number normalized intensities provided by Illumina BeadStudio, Affymetrix powertools, or any similar format. Probes of different samples are split into separate files and can be analyzed on a standalone workstation or in parallel using a cluster/multicore computer. The speed and accuracy of the genome alteration detection analysis (GADA) approach combined with parallel computing results in one of the fastest and most accurate methods, and it is especially suitable to extract copy number alterations (CNAs) on genomewide studies involving hundreds of samples utilizing high density arrays with millions of markers. Functions to perform multivariate analysis and determining common regions among individuals are implemented. Functions to assess association between CNVs blocks and disease is also provided. Useful tools for the summarization and visualization of the discovered CNA are also included. | ||||||||||
| Version: 1.0 | Last change: 2012-02-10 19:33:24+01 | Rev.: 13 | ||||||||||
Download:
 (.tar.gz) |
 (.zip) |
Build status: Current | ||||||||||
R install command:
install.packages("gada", repos="http://R-Forge.R-project.org") | ||||||||||
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Build status codes
0 - Current: the package is available for download. The corresponding package passed checks on the Linux and Windows platform without ERRORs.
1 - Scheduled for build: the package has been recognized by the build system and provided in the staging area.
2 - Building: the package has been sent to the build machines. It will be built and checked using the latest patched version of R. Note that it is included in a batch of several packages. Thus, this process will take some time to finish.
3 - Failed to build: the package failed to build or did not pass the checks on the Linux and/or Windows platform. It is not made available since it does not meet the policies.
4 - Conflicts: two or more packages of the same name exist. None of them will be built. Maintainers are asked to negotiate further actions.
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