source: plugins

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Diff Rev Age Author Log Message
(edit) @1064   13 years Jari Häkkinen Addresses #118. Calculate target with median instead of mean.
(edit) @1063   13 years Jari Häkkinen Add qQuantiler to autodetection list.
(edit) @1062   13 years Jari Häkkinen Addresses #118. Added support to use either mean or median in target …
(edit) @1060   13 years Martin Svensson Fixes #195 Normalizers should ask user for how to calculate averages
(edit) @1059   13 years Jari Häkkinen Use functionality already in yat.
(edit) @1058   13 years Jari Häkkinen The normalizer package now depends in PluginUtilites? version 0.1
(edit) @1057   13 years Jari Häkkinen Tagging version 0.1 of PluginUtilities?
(edit) @1056   13 years Jari Häkkinen Preparing release 0.1 of PluginUtilities? package.
(edit) @1055   13 years Jari Häkkinen Reverting previuos commit on configure.ac, still requiring 0.5.3
(edit) @1054   13 years Jari Häkkinen Cleaned up iterator usage in qQN.cc
(edit) @1053   13 years Jari Häkkinen Addresses #208. Fixing typos.
(edit) @1052   13 years Jari Häkkinen Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.
(edit) @1051   13 years Jari Häkkinen Updated documentation on QuantileNormalization?.
(edit) @1050   13 years Jari Häkkinen Addresses #118. Non-logged input values are expected, geometric mean …
(edit) @1049   13 years Jari Häkkinen Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …
(edit) @1047   13 years Jari Häkkinen Fixes #206. Missing values in reference now works. Each probe with no …
(edit) @1046   13 years Jari Häkkinen Debugging should be turned if in repository code.
(edit) @1045   13 years Jari Häkkinen Missing values now works with the implemented fix to avoid a bug in …
(edit) @1044   13 years Jari Häkkinen Addresses #118 and #206. If no assay data is given use the average of …
(edit) @1043   13 years Jari Häkkinen Addresses #118 and #206. This code produces the same result as the …
(edit) @1042   13 years Jari Häkkinen Changed qqn package name.
(edit) @1041   13 years Jari Häkkinen Changed qqn package name.
(edit) @1040   13 years Jari Häkkinen Use getCurrentBioAssaySet in configuration phase.
(edit) @1039   13 years Jari Häkkinen Fixes #190. target c++ added.
(edit) @1038   13 years Jari Häkkinen Added some detailed information on detection P-calue plug-in
(edit) @1037   13 years Jari Häkkinen Removed duplicated code block.
(edit) @1036   14 years Jari Häkkinen Fixes #197. Abort functionality implemented.
(edit) @1035   14 years Jari Häkkinen Addresses #197. Abort functionality in place in abstract class.
(edit) @1034   14 years Jari Häkkinen Peter says: Use proper classes
(edit) @1032   14 years Nicklas Nordborg Fixes #202: Change source files to UTF-8
(edit) @1031   14 years Jari Häkkinen Joining Nicklas change to UTF-8 frenzy.
(edit) @1030   14 years Nicklas Nordborg Fixes #199: Change source files to UTF-8
(edit) @1029   14 years Jari Häkkinen Joining Nicklas change to UTF-8 frenzy.
(edit) @1023   14 years Jari Häkkinen Addresses #197. In anticipation of abort functionality the underlying …
(edit) @1022   14 years Jari Häkkinen Fixes #184. Progress bar is updated in the abstract class only.
(edit) @1020   14 years Jari Häkkinen Addresses #118 and fixes #187.
(edit) @1014   14 years Jari Häkkinen Fixes #191. Added standard options and also assay annotation data file …
(edit) @1009   14 years Jari Häkkinen Removed non-used configure options inherited from the WeNNI package.
(edit) @1008   14 years Jari Häkkinen Clarified where the recommended install directory is located.
(edit) @1007   14 years Jari Häkkinen metadata is split into reporter and assay metadata. Added flags to …
(edit) @1006   14 years Jari Häkkinen metadata is split into reporter and assay metadata.
(edit) @1005   14 years Jari Häkkinen storeValues typo! Plural importantsvn diff
(edit) @1004   14 years Jari Häkkinen Removed warning suppressions, clean up of code, added missing …
(edit) @1003   14 years Jari Häkkinen Added support to select assays ... but the select is not used yet.
(edit) @1002   14 years Jari Häkkinen Added support to optionally select assays.
(edit) @1001   14 years Jari Häkkinen Minor changes to debug_option.
(edit) @1000   14 years Jari Häkkinen storeResult interface change, some code moved to super class.
(edit) @999   14 years Jari Häkkinen Restructured result storage.
(edit) @998   14 years Jari Häkkinen Addresses #118 and #183. Moved export of data to an export method.
(edit) @997   14 years Jari Häkkinen Tagging version 1.1 of VirtualArray?.
(edit) @996   14 years Jari Häkkinen Preparing release 1.1 of VirtualArray?.
(edit) @993   14 years Jari Häkkinen Addresses #118. First version of working qQuantileNormalizer.
(edit) @992   14 years Jari Häkkinen Require BASE 2.5. Restructure build script.
(edit) @991   14 years Jari Häkkinen Minor things.
(edit) @990   14 years Jari Häkkinen Typo.
(edit) @989   14 years Jari Häkkinen Missing values from BASE are empty fields, need to define field …
(edit) @984   14 years Jari Häkkinen Added support to write to stdin of underlying binary ... added missing …
(edit) @983   14 years Jari Häkkinen Added support to write to stdin of underlying binary.
(edit) @981   14 years Martin Svensson Changed requirements to version 2.9 of BASE both in documentation and …
(edit) @979   14 years Jari Häkkinen 2.9 BASE core API required since changeset:975
(edit) @977   14 years Martin Svensson References #119 Corrected the calculation of relative rank between …
(edit) @975   14 years Martin Svensson References #119 Some changes in the calculation-part. The plug-in runs …
(edit) @973   14 years Jari Häkkinen Addresses #118. Required yat version is 0.5 or later
(edit) @972   14 years Jari Häkkinen Addresses #118. Load of java wrapper works but manual install of …
(edit) @971   14 years Martin Svensson Added library-files to the ignore-list
(edit) @970   14 years Martin Svensson Preparing for future release Illumina package v1.4
(edit) @969   14 years Martin Svensson Tagging release 1.3
(edit) @968   14 years Martin Svensson Preparing release 1.3
(edit) @967   14 years Martin Svensson References #119 The plug-in is mostly ready for testing
(edit) @966   14 years Martin Svensson References #119 Part of the normalization algorithm is implemented
(edit) @965   14 years Jari Häkkinen Corrected flags summary output
(edit) @964   14 years Jari Häkkinen Added support to add qQN source to the normalizer package.
(edit) @963   14 years Jari Häkkinen Improved configure.ac and added option to disable check on required libs.
(edit) @962   14 years Jari Häkkinen Added missing include statement.
(edit) @961   14 years Jari Häkkinen Refs #118 and #161. PluginUtilities? download support. Added distclean …
(edit) @960   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @959   14 years Martin Svensson Fixes #164 Improve documentation on how to upgrade the illumina …
(edit) @958   14 years Martin Svensson Fixes #177 Add information about how to upgrade the normalization package.
(edit) @957   14 years Nicklas Nordborg Fixes #175: Update the ant script to include contrib directory when …
(edit) @956   14 years Jari Häkkinen Removed stray character in configure.ac
(edit) @955   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @954   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @953   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @952   14 years Jari Häkkinen Addresses #118. Added underlying C++ binary for the qQuantile.
(edit) @951   14 years Martin Svensson References #119 Added plugin-class. The plugin doesn't really do …
(edit) @950   14 years Martin Svensson References #119 Moved some method from the QuantileNormalization?
(edit) @949   14 years Martin Svensson Fixes #176 Create release document
(edit) @948   14 years Martin Svensson Fixes #168 MD5 sum should be automatically generated for a package
(edit) @947   14 years Martin Svensson Fixes #166 (net.sf.basedb.normalizers) Automatic progression of …
(edit) @946   14 years Martin Svensson References #161 Set external jar-files to be ignored
(edit) @945   14 years Martin Svensson Fixes #161 (net.sf.basedb.normalizers) Automatic download of BASE API
(edit) @944   14 years Martin Svensson References #173 The 'float to integer' conversion has been removed but …
(edit) @943   14 years Martin Svensson Fixes #171 IBS raw data importer should be able to handle floats in …
(edit) @942   14 years Martin Svensson Fixes #170 Result dialouge after batch importing several raw bioassays …
(edit) @941   14 years Martin Svensson References #174 license text should referr to the Illumina plug-in package
(edit) @940   14 years Martin Svensson Fixes #174 Change license to GPL 3 for the illumina package
(edit) @938   14 years Jari Häkkinen Added svn property.
(edit) @937   14 years Jari Häkkinen Added beadstudio data to IBS data converter.
(edit) @936   14 years Peter Johansson add --force option in autoreconf call in bootstrap. The reason this is …
(edit) @935   14 years Jari Häkkinen Removing braches.
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