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.

Additional array platform support

Illumina plug-ins package: A package of plug-ins for working with Illumina Sentrix and Illumina SNP arrays. Works with BASE 2.9 and later

Analysis

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Filter

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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

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 The Plier algorithm in this plug-in is superseded by the ​APT plug-in.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. Works with BASE 2.7 and later

Quality Control (QC)

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Transformation

WeNNI: Missing value imputation. Not released yet

Un-categorized

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

Web client extensions

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

FTP Server

An extension that adds an FTP server to BASE, making it possible to upload/download files to/from BASE using regular FTP client software. Works with BASE 2.10 and later.

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.

Name	Version	BASE version	Comment
Export
CGH Data Dumper		1.2.17+, 2.8	Dumps bioassay sets in several formats, useful for non-CGH data as well. Not tested with BASE 1.2.17+ but expected to work
Filter
ReplicateError	​1.3 (​MD5)	1.2.17+, 2.8	Not tested with BASE 1.2.17+ but expected to work.
Transformation
Median/mean centering	​2.1 (​MD5)	1.2.17+, 2.8	Not tested with BASE 1.2.17+ but expected to work.
Merge BioAssay	​2.1 (​MD5)	1.2.17+, 2.8	Not tested with BASE 1.2.17+ but expected to work.
Virtual Array	​1.1 (​MD5)	1.2.17+, 2.10	Not tested with BASE 1.2.17+ but expected to work.
WeNNI	​0.6	1.2.17+	Missing value imputation
Other
BaseFile	​1.0 (​MD5)	1.2.17+, 2.8	Java utility package for reading the BASEFile format. Required for many se.lu.onk-series plug-ins. Not tested with BASE 1.2.17+ but expected to work.

Quality Control (QC)

Transformation

Smooth: Works with BASE 1.2.17+

Normalization

popLowess: Works with BASE 1.2.17+

Analysis

One class Z-test: Works with BASE 1.2.17+