R Development Page
Contributed R Packages
Below is a list of all packages provided by project aroma.* packages [MOVED TO GITHUB].
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).
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EBImage | DUMMY DUMMY DUMMY
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DO NOT INSTALL THIS PACKAGE. If you wish to install EBImage, please go to http://www.bioconductor.org/ website and follow the instructions over there. THIS IS AN EMPTY PACKAGE WITH THE SAME NAME AS AN EXISTING BIOC PACKAGE. THE ONLY PURPOSE OF THIS PACKAGE IS TO PREVENT THE R-FORGE BUILD SERVERS TO HALT THE BUILDING OF AROMA.CORE AND AROMA.AFFYMETRIX. THIS DUMMY PACKAGE WILL NOT BE NEEDED WHEN R-FORGE INCLUDES THE REAL EBIMAGE PACKAGE OR SETS R_check_force_suggests=false |
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Version: 0.0.1 |
Last change: 2015-01-07 18:28:11+01 |
Rev.: 3677 |
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Download:
 (.tar.gz) |
 (.zip) |
Build status: Current |
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R install command:
install.packages("EBImage", repos="http://R-Forge.R-project.org") |
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aroma.Base | A generic R plugin dispatcher for BASE
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This package provides R methods to interact with BioArray Software Environment (BASE). The BaseFile class provides an API for easy to loading, retrieving, modifying, and saving BASE files. The static class BasePluginDispatcher is used to call R plugins by taking care of importing data from BASE, automatic exception handling, logging to file, returning data to BASE etc. |
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Version: 0.4.8 |
Last change: 2009-09-18 19:47:22+02 |
Rev.: 1652 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Failed to build |
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R install command:
install.packages("aroma.Base", repos="http://R-Forge.R-project.org") |
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aroma.agilent | Analysis of Agilent microarray data [A DRAFT - TRUE]
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This package provides method for analysis of Agilent data. |
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Version: 0.1.2 |
Last change: 2013-03-09 04:51:15+01 |
Rev.: 2968 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Failed to build |
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R install command:
install.packages("aroma.agilent", repos="http://R-Forge.R-project.org") |
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aroma.apd | A probe-level data file format used by aroma.affymetrix [DEPRECATED]
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THIS PACKAGE HAS BEEN DEPRECATED. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.) |
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Version: 0.5.0 |
Last change: 2014-06-15 04:39:43+02 |
Rev.: 3668 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get aroma.apd 0.7.1 from CRAN |
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R install command:
install.packages("aroma.apd", repos="http://R-Forge.R-project.org") |
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aroma.seq | High-throughput sequence (HT-Seq) analysis in the Aroma framework
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Simple, flexible and distributed processing of very large-scale HT-Seq data - available at the R prompt. [RATHER EARLY VERSION] |
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Version: 0.5.8 |
Last change: 2014-06-15 08:46:45+02 |
Rev.: 3673 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Failed to build |
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R install command:
install.packages("aroma.seq", repos="http://R-Forge.R-project.org") |
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aroma.tcga | Methods for accessing online The Cancer Genome Atlas (TCGA) data
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Utility functions for accessing the public and protected data files at the The Cancer Genome Atlas (TCGA) Data Collection Center (DCC). This package is very much in an alpha stage where the API keeps changing from day to day. |
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Version: 0.5.3 |
Last change: 2010-04-05 17:59:58+02 |
Rev.: 1948 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current |
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R install command:
install.packages("aroma.tcga", repos="http://R-Forge.R-project.org") |
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cnagIO | Methods for reading CNAG files
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This package provides methods for reading CFH files generated by the CNAG software. |
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Version: 0.1.3 |
Last change: 2014-06-17 02:50:30+02 |
Rev.: 3676 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current |
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R install command:
install.packages("cnagIO", repos="http://R-Forge.R-project.org") |
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dChipIO | Methods for reading dChip files
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This package provides methods for reading DCP and CDF.bin files generated by the dChip software. |
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Version: 0.1.2 |
Last change: 2014-06-16 23:33:39+02 |
Rev.: 3675 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Current | Stable Release: Get dChipIO 0.1.5 from CRAN |
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R install command:
install.packages("dChipIO", repos="http://R-Forge.R-project.org") |
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illuminaIO | Low-level methods for reading Illumina data files
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[DEPRECATED: As of Oct 2012, this package has been deprecated in favor the the Bioconductor illuminaio package, cf. http://www.bioconductor.org/packages/devel/bioc/html/illuminaio.html] Low-level methods for reading Illumina data files |
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Version: 0.2.2 |
Last change: 2013-03-09 04:54:59+01 |
Rev.: 2976 |
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Download:
(.tar.gz) |
(.zip) |
Build status: Failed to build |
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R install command:
install.packages("illuminaIO", 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.
5 - Offline: the package is not available. The build system may be offline or the package maintainer did not trigger a rebuild (done e.g., via committing to the package repository).
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