wiki:PluginDownload

Version 63 (modified by martin, 9 years ago) (diff)

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Plug-in and extensions download

This page provides easy access to BASE 1 and 2 plug-ins for users who prefer not to use the subversion repository for downloading the plug-ins

The latest stable BASE can be downloaded from the BASE 2 development site. The latest BASE 1 release is available from BASE 1.2.x development site and the latest BASE 1.2 plug-in development kit may be needed for some of the BASE 1 plug-ins.

BASE 2

Plug-ins

Plug-ins created for BASE 2 do not work with BASE 1.x.

Quality Control (QC)
Transformation
WeNNI: Missing value imputation. Not released yet
Normalization
Affymetrix plug-in for BASE: Affymetrix normalization with RMAExpress or Plier (download latest MD5). The Plier algorithm in this plug-in is superseded by the APT plug-in. Works with BASE 2.0 and later
APT: Affymetrix Power Tools execution plug-in. Currently apt-probeset-summarize and apt-probeset-geneotype from APT is acccessible through this plug-in. Works with BASE 2.4 and later
Normalization package: A package with different kinds of normalization plug-ins. Not released yet.
Filter
Analysis
Import/Export?
AffyArrayDesignBatchImporter: Imports batches of affymetrix array design into base 2. Works with BASE 2.2 and later
AnnotationTypeCvImporter: Import annotation type annd controlled vocabularies from a simple flat file into base 2. Works with BASE 2.0 and later
BatchDataImporter: Imports batches of data files into BASE, creating a single RawbioAssay for each file. Works with BASE 2.2 and later
Tab2MageExporter: Exports an experiment meta-data in the tab2mage specification from base 2. Works with BASE 2.2 and later
Tab2MageImporter: Imports raw data files and an experiment meta-data in the tab2mage specification into base 2. Works with BASE 2.2 and later
Other
BAFsegmentation: Segments B allele frequencies from SNP arrays to identify regions of allelic imbalance. Not released yet
GCRMA: Works with BASE 2.0 and later
Illumina plug-ins package: A package of plug-ins for working with Illumina Sentrix and Illumina SNP arrays. Works with BASE 2.6 and later

Web client extensions

An extension mechanism was introduced in the BASE 2.7 web client. Extensions are used for adding functionality the GUI, such as extra menus and buttons.

MEV Launcher
Integrates BASE with TIGR MultiExperiment Viewer (MEV). Works with BASE 2.7 and later.
Example extensions?
A package with several "Hello world" examples of extensions to the web client. Works with BASE 2.7 and later.

Example code

Plug-ins
Example plug-ins for BASE2: A package with example plug-ins intended for the developer. Works with BASE 2.6 and later
Web services
Web services examples for BASE 2: A package with a Java client application that uses web services to get information from a BASE 2 server. Works with BASE 2.6 and later
Extensions
Example extensions for the BASE web client?: A package with several "Hello world" examples of extensions to the web client. Works with BASE 2.7 and later.

External BASE 2 plug-in developer sites

The MicroArray Datawarehouse Resource@LCB develops BASE plug-ins, please visit their development site at http://madr.lcb.uu.se/.

BASE 1.2 plug-ins

Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plug-in.

Quality Control (QC)
Export
CGH Data Dumper: Dumps bioassay sets in several formats, useful for non-CGH data as well. Works with BASE 1.2.17+
Transformation
Merge BioAssay: Works with BASE 1.2.17+
Smooth: Works with BASE 1.2.17+
WeNNI: Missing value imputation (download latest). Works with BASE 1.2.17+
Normalization
popLowess: Works with BASE 1.2.17+
Filter
Analysis
One class Z-test: Works with BASE 1.2.17+
Other

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