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Ticket Summary Status Owner Type Priority Milestone
#229 Implement API for additional GenePattern web services assigned Nicklas Nordborg task critical ZZ GenePattern integration v1.0
#267 Change qQuantilerNormalization underlying binary to use the new BFS format assigned Jari Häkkinen task critical Normalization package v1.1
#1119 Re-implement TIFF to JPG conversion for Histology images using the ImageIO API new Nicklas Nordborg enhancement critical Reggie v4.x
#43 Add request for proper default permissions (se.lu.thep.affymetrix). new Jari Häkkinen enhancement major ZZ Other tickets
#50 create a BASE2 plug-in for se.lu.thep.WeNNI assigned Jari Häkkinen task major se.lu.thep.wenni 0.7
#70 Add releasing procedure to se.lu.thep.affymetrix new Jari Häkkinen task major ZZ Other tickets
#78 Spike Lowess (se.lu.onk.lowess) new Jari Häkkinen task major ZZ Other tickets
#80 QQPlot new Jari Häkkinen task major ZZ Other tickets
#81 Merge on genesymbol new Jari Häkkinen task major ZZ Other tickets
#82 COPA new Jari Häkkinen task major ZZ Other tickets
#85 Pinbased normalization for VirtualArray data new Jari Häkkinen enhancement major ZZ Other tickets
#86 BasicReporter and BasicSpot (se.lu.onk.BaseFile) new Jari Häkkinen enhancement major ZZ Other tickets
#87 AnnotationFilter (se.lu.onk.AnnotationFilter) new Jari Häkkinen defect major ZZ Other tickets
#96 Make the se.lu.thep.affymetrix plug-in compatible with the auto-installation wizard new Jari Häkkinen enhancement major ZZ Other tickets
#119 Create rank invariant normalizer reopened Martin Svensson task major Normalization package v1.1
#144 R plug-in framework new Johan Enell task major ZZ A wish list
#147 WeNNI for BASE2 should support the automatic plug-in installation feature of BASE new Jari Häkkinen enhancement major se.lu.thep.wenni 0.7
#153 Autoconf issues in se.lu.thep.WeNNI new Peter Johansson task major se.lu.thep.wenni 0.7
#160 wenni and the underlying super class should be abortable (se.lu.thep.WeNNI) assigned Jari Häkkinen enhancement major se.lu.thep.wenni 0.7
#169 Running two "New root bioassay set" jobs at the same time makes the second to finish crash new Jari Häkkinen defect major ZZ Other tickets
#172 Why is there a check for LIBTOOL in configure.ac in the WeNNI project? new Jari Häkkinen task major se.lu.thep.wenni 0.7
#185 External binary plugins should be interruptable from BASE. assigned Jari Häkkinen enhancement major ZZ Other tickets
#188 Add IGV as an extension similarly to MEV new Jari Häkkinen task major ZZ A wish list
#209 Export of data to data repositories such as GEO and ArrayExpress new Jari Häkkinen task major ZZ A wish list
#210 net.sf.basedb.normalizers: Add proper 2-channel support to qQuantileNormalizer new Jari Häkkinen defect major Normalization package v1.2
#211 Request: R/G quantile normalization new Martin Svensson Request major ZZ A wish list
#218 Proof-of-concept: run a selected GenePattern module from BASE assigned Nicklas Nordborg task major ZZ GenePattern integration v1.0
#219 Setup a GenePattern server for testing new Nicklas Nordborg task major ZZ GenePattern integration v1.0
#225 qQuantiler should select all assays as reference by default assigned Jari Häkkinen Request major Normalization package v1.1
#234 Proof-of-concept: run a selected GenePattern visualization module from BASE assigned Nicklas Nordborg task major ZZ GenePattern integration v1.0
#244 Create a SAM plug-in new Jari Häkkinen Request major ZZ A wish list
#250 Add GSEA as an extension new Jari Häkkinen Request major ZZ A wish list
#253 GeneSpring connector new Jari Häkkinen Request major ZZ A wish list
#254 Is Chipster something for BASE, should it be integrated similarly to MeV new Jari Häkkinen Request major ZZ A wish list
#256 Java web start enable data visualizer new Jari Häkkinen Request major ZZ A wish list
#260 Restructure tab2mage repository such that releases can be tagged new Jari Häkkinen task major ZZ Other tickets
#261 Create proper release packages of tab2mage plugins new Jari Häkkinen task major ZZ Other tickets
#262 Tab2Mage exporter exception: Can't use an unsaved item in query: Annotation set[new] new Jari Häkkinen defect major ZZ Other tickets
#268 Refactor qQuantileNormalizer plugin to use the ExternalProgramExecutor plugin assigned Jari Häkkinen task major Normalization package v1.1
#306 Create package for supporting external files on Amazon S3 new Jari Häkkinen Request major ZZ A wish list
#325 Import files from a HDFS directory as external file items new Nicklas Nordborg task major ZZ HDFS package v1.1
#413 Handle re-running a sample on Caliper with Hi-Sense option new Nicklas Nordborg enhancement major Reggie v4.x
#463 Illumina expression background correction (version 1.7) does not ask for required permissions to write file new Jari Häkkinen defect major Illumina package v1.8
#476 Get list of blood samples where at least one RNA extract exists new Nicklas Nordborg task major Reggie v4.x
#510 Consistent use of terms in the lab protocols and Reggie interface new johan enhancement major Reggie v4.x
#531 BASE1 plugin - Transformation: Merge replicates new Jari Häkkinen enhancement major ZZ Other tickets
#532 reggie QC wizard for additional QC measurements outside of routine new Nicklas Nordborg Request major Reggie v4.x
#584 Make it possible to use different volumes for different RNA in Create mRNA plate wizard new Nicklas Nordborg enhancement major Reggie v4.x
#585 Cluster start date shold be a date+time annotation new Nicklas Nordborg enhancement major Reggie v4.x
#586 Register end date+time for clustering new Nicklas Nordborg enhancement major Reggie v4.x
#588 Update extensions to target Java 1.7 and BASE 3.3 new Jari Häkkinen task major
#695 New reporter annotations new Nicklas Nordborg enhancement major Reggie v4.x
#696 Implement some skin examples for BASE new task major Skin-collection 1.0
#752 Schedule new RNAQC from Flagged RNA wizard new Nicklas Nordborg enhancement major Reggie v4.x
#1029 MeLuDI should be adapted to support the SCAN-B-rec project assigned olle task major MeLuDI v1.6.0
#1146 Demux for the MIPs pipeline accepted Nicklas Nordborg task major Reggie v4.23
#1159 Release exporter changes due to MIPs pipeline new Nicklas Nordborg enhancement major Reggie v4.23
#39 create reporter list (se.lu.onk.ztest) new Jari Häkkinen enhancement minor ZZ Other tickets
#56 rename component onk.lu.se to be se.lu.onk -- split into several packages new Jari Häkkinen defect minor ZZ Other tickets
#71 write HowToRelease document for se.lu.thep.WeNNI new Peter Johansson task minor se.lu.thep.wenni 0.7
#919 Include information about deliverd reports in case summary new Nicklas Nordborg enhancement minor Reggie v4.x
#1157 Case summary changes due to MIPs pipeline accepted Nicklas Nordborg enhancement minor Reggie v4.23
#1172 The message in the "Secondary analysis cleanup" wizard is confusing new Nicklas Nordborg enhancement minor Reggie v4.23
#74 unmappable character for encoding UTF8 Copyright (C) Jari Häkkinen (se.lu.thep.affymetrix) new Jari Häkkinen defect trivial ZZ Other tickets
#158 README in PluginUtilities refers to AbstractRunBinary.jar assigned Jari Häkkinen defect trivial ZZ Other tickets
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