source: plugins/base2

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Diff Rev Age Author Log Message
(edit) @873   14 years Nicklas Nordborg Fixes #151: Use two queries instead of one in DetectionPValue.run() method
(edit) @862   14 years Jari Häkkinen Cleanup of the abstract super class. More to come …
(edit) @861   14 years Jari Häkkinen Using BASE 2.9 API
(edit) @847   14 years Jari Häkkinen Renamed package to PluginUtilities?.
(edit) @833   14 years Nicklas Nordborg Fixes #150: Fix layout of DetectionPValue.java
(edit) @829   14 years Jari Häkkinen Setting svndigest:ignore on copies of trunks to avoid multiple counting.
(edit) @818   14 years Jari Häkkinen First commit of the AbstractRunBinaryPlugin? class. Still very …
(edit) @817   14 years Jari Häkkinen Fixing typo.
(edit) @816   14 years Martin Svensson References #143 Removed unnecessary comments.
(edit) @815   14 years Martin Svensson Fixes #143 Illumina plug-in package installer requests wrong permissions
(edit) @814   14 years Nicklas Nordborg References #142. Removed problematic character. For historical reasons …
(edit) @813   14 years Martin Svensson Fixes #142 Illumina installer plugin cannot be installed in some cases
(edit) @812   14 years Jari Häkkinen Creating a new package.
(edit) @811   14 years Martin Svensson Fixes #141 Rank invariant should not support configurations. The …
(edit) @810   14 years Nicklas Nordborg Fixes #138: Importing data for multiple raw bioassays in one step
(edit) @809   14 years Nicklas Nordborg Updated release doc so we don't forget version information in …
(edit) @808   14 years Nicklas Nordborg References #110: Illumina detection P-value plug-in Static method in …
(edit) @807   14 years Nicklas Nordborg Fixes #140: Add support in build.xml for automatic download of BASE …
(edit) @755   14 years Martin Svensson Fixed weaknesses discovered with FindBugs?-eclipse plug-in
(edit) @754   14 years Martin Svensson References #119 Change to only create a row summary array if it has …
(edit) @753   14 years Martin Svensson The SpotData2Ch objects are now compared by their ratio-value and not …
(edit) @752   14 years Martin Svensson Fixes #119 Create Rank Invariant normalization
(edit) @751   14 years Martin Svensson References #119 Bug-fixing
(edit) @750   14 years Martin Svensson References # 119 The normalization algorithm is almost done. Some …
(edit) @749   14 years Martin Svensson References # 119 Started with the development of this plug-in. No …
(edit) @748   14 years Martin Svensson Fixes #117 Create average nomralization plug-in.
(edit) @747   14 years Martin Svensson References #124 Corrected a few more copy-paste mistake.
(edit) @746   14 years Martin Svensson Fixes #124 Corrected a copy-paste mistake. Also added …
(edit) @745   14 years Martin Svensson References #117 Bug-fixing
(edit) @744   14 years Martin Svensson References #117 Corrected a package name. Also changed the way global …
(edit) @743   14 years Martin Svensson References #117 The normalization is now done. Nothing has been tested …
(edit) @742   14 years Martin Svensson References #117 Cleaned up and refactored the classes. The Avg.norm. …
(edit) @740   14 years Martin Svensson Change name of the package
(edit) @739   14 years Martin Svensson Added new files to the project such as license file, library-files and …
(edit) @738   14 years Martin Svensson Added BASE2WSClient.jar to svn:ignore
(edit) @737   14 years Martin Svensson Fixes #121 BGX-importer should 0-pad Array_Address_ID if the BGX-file …
(edit) @736   14 years Martin Svensson Fixes #112. Changed the property validation when installing a data …
(edit) @735   14 years Martin Svensson Correct the layout
(edit) @734   14 years Martin Svensson Changed the svn-properties so the pages can be viewed in the wiki
(edit) @733   14 years Martin Svensson References #122 Created README and INSTALL pages for the Normalization …
(edit) @732   14 years Martin Svensson References #112 Changed the exception message.
(edit) @731   14 years Martin Svensson Re-arrange in build file for the Normalization plug-in package.
(edit) @730   14 years Martin Svensson References #117 Average normalization plug-in is almost done. The …
(edit) @729   14 years Martin Svensson References #117 Almost done with implementing the normalization …
(edit) @728   14 years Martin Svensson Re-arrange the files. Created the plug-in body for average and cubic …
(edit) @727   14 years Martin Svensson First commit of the normalization package. Contains folder structure, …
(edit) @726   14 years Martin Svensson
(edit) @725   14 years Martin Svensson
(edit) @724   14 years Martin Svensson
(edit) @723   14 years Martin Svensson Added a folder for the normalization package.
(edit) @718   14 years Jari Häkkinen Also share manifest file.
(edit) @703   14 years Jari Häkkinen Preparing for future 1.2 release
(edit) @702   14 years Jari Häkkinen Tagging release 1.1
(edit) @701   14 years Jari Häkkinen Preparing release of Illumina plug-in package 1.1
(edit) @700   14 years Jari Häkkinen Improved description.
(edit) @699   14 years Jari Häkkinen Added two new plugins to the list of plugins. Alphabetized list.
(edit) @698   14 years Jari Häkkinen Fixes #110.
(edit) @689   14 years Jari Häkkinen Addresses #110. Added MAD based outlier removal of negative control …
(edit) @688   14 years Jari Häkkinen Typo
(edit) @686   14 years Jari Häkkinen Addresses #110.
(edit) @685   14 years Jari Häkkinen Improved text.
(edit) @684   14 years Jari Häkkinen Fixes #104. Docs already fixed, added build check.
(edit) @681   14 years Jari Häkkinen Addresses #110. Single sample Whole Genome BeadChips? detection P-value …
(edit) @680   14 years Jari Häkkinen Bumped version number to pre1.1
(edit) @679   14 years Jari Häkkinen Moving flush call to a more appropriate place.
(edit) @678   14 years Jari Häkkinen No configurations for BeadSummaryImporter?
(edit) @677   14 years mbayer tidied up -- minor changes
(edit) @676   14 years mbayer removed deprecated code for raw bioassay creation and replaced with …
(edit) @675   14 years mbayer default values for update existing parameter changed
(edit) @674   14 years mbayer changed the way the zip file input stream is obtained back to how it was
(edit) @673   14 years mbayer updated
(edit) @672   14 years mbayer removed default values for most inputs
(edit) @671   14 years mbayer added code for copying over the two additional required jar files …
(edit) @670   14 years mbayer - build script tidied up - new BASE libs added and existing ones …
(edit) @669   14 years Jari Häkkinen Adding background correction plugin
(edit) @660   14 years Jari Häkkinen Alphabetized list and fixed indendation.
(edit) @659   14 years mbayer fixed two minor errors in build script
(edit) @655   14 years mbayer deleted this jar file -- it does not get updated! need to use …
(edit) @654   14 years mbayer have made a number of changes relating to Affy support and fixed …
(edit) @650   14 years Nicklas Nordborg Preparing for future release 2.X
(edit) @649   14 years Nicklas Nordborg Tagging release 2.6
(edit) @648   14 years Nicklas Nordborg Preparing relase 2.6
(edit) @647   14 years Nicklas Nordborg References #105: Complete the move of the example code from BASE. …
(edit) @646   14 years Jari Häkkinen Fixing copyright lines.
(edit) @645   14 years Jari Häkkinen Updated the BASE core jar requirements.
(edit) @644   14 years mbayer have added a progress bar to the userchoice3.jsp page to warn the user …
(edit) @643   14 years mbayer code base simplified -- no longer supporting autogenerate option and …
(edit) @640   14 years mbayer test file commit -- having trouble committing into the new repo
(edit) @639   14 years mbayer simplified the workflow and inputs
(edit) @634   14 years Nicklas Nordborg Added release procedure instructions.
(edit) @633   14 years Nicklas Nordborg Changes for future release 1.1
(edit) @632   14 years Nicklas Nordborg Tagging release 1.0
(edit) @631   14 years Nicklas Nordborg References #91: Import Illumina Bead Summary(IBS) files as raw data …
(edit) @630   14 years Nicklas Nordborg References #94: Import reporter annotations from bgx files Added …
(edit) @629   14 years Nicklas Nordborg References #89: Installation program and documentation Preparing for …
(edit) @628   14 years Nicklas Nordborg References #89: Installation program and documentation Made the SNP …
(edit) @627   14 years Nicklas Nordborg References #89: Installation program and documentation Added readme …
(edit) @626   14 years Nicklas Nordborg References #89, #100: Added formulas for better SNP gui. Gtype = …
(edit) @625   14 years Nicklas Nordborg References #102: Intensity calculator for Illumina SNP data Added …
(edit) @624   14 years Nicklas Nordborg References #102: Intensity calculator for Illumina SNP data The main …
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