Version 0.8.1 Date 2010-04-22 Title Easy handling of and access to files organized in structured directories

Description A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate suchs sets. The API is designed such that these classes can be subsetted to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have fullnames which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package’s API should be considered to be in an beta stage. Its main purpose is currently to support the aroma. * packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first. License LGPL (> = 2.1

Version 0.4.5 Date 2011-03-08 Title R Server

Description An R Server Page (RSP) is a document that contains both text in a format of choice (HTML, TeX, Rnw,...) as well as R source code within special tags. An RSP file can be translated into a so called R servlet, which is an R script that outputs the final document when sourced. This way documents in any format can be generated dynamically using R, e.g. automatic reports of statistical analysis. Utilizing an internal cross-platform web server, this package provides dynamic help pages in HTML. If other packages provide RSP help pages, these are automatically linked to in the RSP main menu. License LGPL (> = 2.1

Repository CRAN

Description This package provides utility classes and methods useful when programming in R and developing R packages

Version 2.0.0 Date 2011-02-16 Title Core methods and classes used by aroma. * package part of The Aroma Project

Imports affxparser (> = 1.16.0), RColorBrewer (> = 1.0-2) Suggests RColorBrewer (> = 1.0-2), png (> = 0.1-2), EBImage (> = 2.2.0),Cairo (> = 1.3-5), sfit (> = 0.1.8), expectile (> = 0.2.5), GLAD (> = 1.12.0), DNAcopy (> = 1.20.0), HaarSeg (> = 0.0.2), mpcbs (> = 1.1.1) Description 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 should be considered to be in alpha and beta versions, and is mostly of interest to developers. License LGPL (> = 2.1

Imports methods

Suggests tool

Description THIS PACKAGE HAS BEEN DEPRECATED. Do not start building

new projects based on it. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (BioConductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.) License LGPL (> = 2.1

Version 1.4.2 Date 2012-06-22 Title Utility function for defining S3 methods

Description Methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4. This is a cross-platform package implemented in pure R that generates standard S3 methods. License LGPL (> = 2.1

Date 2013-01-17 Title Easy handling of and access to files organized in structured directories

Description A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package’s API should be considered to be in an beta stage. Its main purpose is currently to support the aroma. * packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first. License LGPL (> = 2.1

Version 0.1.8 Date 2011-01-31

format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensites. 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 speed up the read substantially. This package is supporting the aroma.affymetrix package and not intended to be used elsewhere.) License LGPL (> = 2.1

License LGPL (> = 2.1)

Description Methods for memoization, that is, caching arbitrary R objects in persistent memory. Objects can be loaded and saved stratified on a set of hashing objects