SCM

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).

Packages

EBImage

DUMMY DUMMY DUMMY

  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
  Version: 0.0.1 | Last change: 2015-01-07 18:28:11+01 | Rev.: 3677
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current
  R install command: install.packages("EBImage", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


aroma.Base

A generic R plugin dispatcher for BASE

  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.
  Version: 0.4.8 | Last change: 2009-09-18 19:47:22+02 | Rev.: 1652
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("aroma.Base", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


aroma.affymetrix

Analysis of large Affymetrix microarray data sets

  This package implements classes for files and sets of files for various Affymetrix file formats, e.g. AffymetrixCdfFile, AffymetrixCelFile, and AffymetrixCelSet. These are designed to be memory efficient but still being fast. The idea is to keep all data on file and only read data into memory when needed. Clever caching mechanisms are used to minimize the overhead of data IO. All of the above is hidden in the package API and for the developer (and the end user), the data is queried as if it lives in memory. With this design it is only the disk space that limits the number of arrays that can be analyzed.
  Version: 2.12.4 | Last change: 2014-06-15 05:20:58+02 | Rev.: 3669
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build | Stable Release: Get aroma.affymetrix 3.1.1 from CRAN
  R install command: install.packages("aroma.affymetrix", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


Old Version: 2.12.4 | Last change: 2015-11-10 12:04:28
Old Version Download: linux(.tar.gz) | windows(.zip)

aroma.agilent

Analysis of Agilent microarray data [A DRAFT - TRUE]

  This package provides method for analysis of Agilent data.
  Version: 0.1.2 | Last change: 2013-03-09 04:51:15+01 | Rev.: 2968
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("aroma.agilent", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


aroma.apd

A probe-level data file format used by aroma.affymetrix [DEPRECATED]

  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.)
  Version: 0.5.0 | Last change: 2014-06-15 04:39:43+02 | Rev.: 3668
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current | Stable Release: Get aroma.apd 0.6.0 from CRAN
  R install command: install.packages("aroma.apd", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


aroma.axon

Analysis of Axon GenePix microarray data [A DRAFT - TRUE]

  Analysis of Axon GenePix microarray data [A DRAFT - TRUE]
  Version: 0.1.4 | Last change: 2013-03-09 04:52:12+01 | Rev.: 2970
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("aroma.axon", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


Old Version: 0.1.4 | Last change: 2015-11-10 12:04:28
Old Version Download: linux(.tar.gz) | windows(.zip)

aroma.cn

Copy-number analysis of large microarray data sets

  Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
  Version: 1.5.7 | Last change: 2014-06-15 05:23:58+02 | Rev.: 3670
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build | Stable Release: Get aroma.cn 1.6.1 from CRAN
  R install command: install.packages("aroma.cn", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


Old Version: 1.5.7 | Last change: 2015-11-10 12:04:28
Old Version Download: linux(.tar.gz) | windows(.zip)

aroma.cn.eval

Package for evaluating copy-number estimates

  This package is a private for now.
  Version: 0.5.2 | Last change: 2014-06-15 06:13:59+02 | Rev.: 3671
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("aroma.cn.eval", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


Old Version: 0.5.2 | Last change: 2014-06-27 21:36:35
Old Version Download: linux(.tar.gz) | windows(.zip)

aroma.core

Core methods and classes used by aroma.* packages part of The Aroma Framework

  This package contains core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn. Its API is mostly of interest to developers and is rarely used by end users directly.
  Version: 2.12.4 | Last change: 2014-06-15 03:10:34+02 | Rev.: 3665
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build | Stable Release: Get aroma.core 3.1.3 from CRAN
  R install command: install.packages("aroma.core", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


Old Version: 2.12.4 | Last change: 2015-11-10 12:04:28
Old Version Download: linux(.tar.gz) | windows(.zip)

aroma.illumina

Analysis of Illumina microarray data [A DRAFT - TRUE]

  This package provides method for analysis of Illumina data.
  Version: 0.2.1 | Last change: 2013-03-09 04:53:10+01 | Rev.: 2972
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("aroma.illumina", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


Old Version: 0.2.1 | Last change: 2015-11-10 12:04:28
Old Version Download: linux(.tar.gz) | windows(.zip)

aroma.seq

High-throughput sequence (HT-Seq) analysis in the Aroma framework

  Simple, flexible and distributed processing of very large-scale HT-Seq data - available at the R prompt. [RATHER EARLY VERSION]
  Version: 0.5.8 | Last change: 2014-06-15 08:46:45+02 | Rev.: 3673
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("aroma.seq", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


aroma.tcga

Methods for accessing online The Cancer Genome Atlas (TCGA) data

  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.
  Version: 0.5.3 | Last change: 2010-04-05 17:59:58+02 | Rev.: 1948
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current
  R install command: install.packages("aroma.tcga", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


cnagIO

Methods for reading CNAG files

  This package provides methods for reading CFH files generated by the CNAG software.
  Version: 0.1.3 | Last change: 2014-06-17 02:50:30+02 | Rev.: 3676
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current
  R install command: install.packages("cnagIO", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


dChipIO

Methods for reading dChip files

  This package provides methods for reading DCP and CDF.bin files generated by the dChip software.
  Version: 0.1.2 | Last change: 2014-06-16 23:33:39+02 | Rev.: 3675
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current | Stable Release: Get dChipIO 0.1.5 from CRAN
  R install command: install.packages("dChipIO", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


illuminaIO

Low-level methods for reading Illumina data files

  [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
  Version: 0.2.2 | Last change: 2013-03-09 04:54:59+01 | Rev.: 2976
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("illuminaIO", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)

 

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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