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Ticket Summary Status Owner Type Milestone Priority
#43 Add request for proper default permissions (se.lu.thep.affymetrix). new Jari Häkkinen enhancement ZZ Other tickets major
#50 create a BASE2 plug-in for se.lu.thep.WeNNI assigned Jari Häkkinen task se.lu.thep.wenni 0.7 major
#70 Add releasing procedure to se.lu.thep.affymetrix new Jari Häkkinen task ZZ Other tickets major
#78 Spike Lowess (se.lu.onk.lowess) new Jari Häkkinen task ZZ Other tickets major
#80 QQPlot new Jari Häkkinen task ZZ Other tickets major
#81 Merge on genesymbol new Jari Häkkinen task ZZ Other tickets major
#82 COPA new Jari Häkkinen task ZZ Other tickets major
#85 Pinbased normalization for VirtualArray data new Jari Häkkinen enhancement ZZ Other tickets major
#86 BasicReporter and BasicSpot (se.lu.onk.BaseFile) new Jari Häkkinen enhancement ZZ Other tickets major
#87 AnnotationFilter (se.lu.onk.AnnotationFilter) new Jari Häkkinen defect ZZ Other tickets major
#96 Make the se.lu.thep.affymetrix plug-in compatible with the auto-installation wizard new Jari Häkkinen enhancement ZZ Other tickets major
#119 Create rank invariant normalizer reopened Martin Svensson task Normalization package v1.1 major
#144 R plug-in framework new Johan Enell task ZZ A wish list major
#147 WeNNI for BASE2 should support the automatic plug-in installation feature of BASE new Jari Häkkinen enhancement se.lu.thep.wenni 0.7 major
#153 Autoconf issues in se.lu.thep.WeNNI new Peter Johansson task se.lu.thep.wenni 0.7 major
#160 wenni and the underlying super class should be abortable (se.lu.thep.WeNNI) assigned Jari Häkkinen enhancement se.lu.thep.wenni 0.7 major
#169 Running two "New root bioassay set" jobs at the same time makes the second to finish crash new Jari Häkkinen defect ZZ Other tickets major
#172 Why is there a check for LIBTOOL in configure.ac in the WeNNI project? new Jari Häkkinen task se.lu.thep.wenni 0.7 major
#185 External binary plugins should be interruptable from BASE. assigned Jari Häkkinen enhancement ZZ Other tickets major
#188 Add IGV as an extension similarly to MEV new Jari Häkkinen task ZZ A wish list major
#209 Export of data to data repositories such as GEO and ArrayExpress new Jari Häkkinen task ZZ A wish list major
#210 net.sf.basedb.normalizers: Add proper 2-channel support to qQuantileNormalizer new Jari Häkkinen defect Normalization package v1.2 major
#211 Request: R/G quantile normalization new Martin Svensson Request ZZ A wish list major
#218 Proof-of-concept: run a selected GenePattern module from BASE assigned Nicklas Nordborg task ZZ GenePattern integration v1.0 major
#219 Setup a GenePattern server for testing new Nicklas Nordborg task ZZ GenePattern integration v1.0 major
#225 qQuantiler should select all assays as reference by default assigned Jari Häkkinen Request Normalization package v1.1 major
#234 Proof-of-concept: run a selected GenePattern visualization module from BASE assigned Nicklas Nordborg task ZZ GenePattern integration v1.0 major
#244 Create a SAM plug-in new Jari Häkkinen Request ZZ A wish list major
#250 Add GSEA as an extension new Jari Häkkinen Request ZZ A wish list major
#253 GeneSpring connector new Jari Häkkinen Request ZZ A wish list major
#254 Is Chipster something for BASE, should it be integrated similarly to MeV new Jari Häkkinen Request ZZ A wish list major
#256 Java web start enable data visualizer new Jari Häkkinen Request ZZ A wish list major
#260 Restructure tab2mage repository such that releases can be tagged new Jari Häkkinen task ZZ Other tickets major
#261 Create proper release packages of tab2mage plugins new Jari Häkkinen task ZZ Other tickets major
#262 Tab2Mage exporter exception: Can't use an unsaved item in query: Annotation set[new] new Jari Häkkinen defect ZZ Other tickets major
#268 Refactor qQuantileNormalizer plugin to use the ExternalProgramExecutor plugin assigned Jari Häkkinen task Normalization package v1.1 major
#306 Create package for supporting external files on Amazon S3 new Jari Häkkinen Request ZZ A wish list major
#325 Import files from a HDFS directory as external file items new Nicklas Nordborg task ZZ HDFS package v1.1 major
#413 Handle re-running a sample on Caliper with Hi-Sense option new Nicklas Nordborg enhancement Reggie v4.x major
#463 Illumina expression background correction (version 1.7) does not ask for required permissions to write file new Jari Häkkinen defect Illumina package v1.8 major
#476 Get list of blood samples where at least one RNA extract exists new Nicklas Nordborg task Reggie v4.x major
#510 Consistent use of terms in the lab protocols and Reggie interface new johan enhancement Reggie v4.x major
#531 BASE1 plugin - Transformation: Merge replicates new Jari Häkkinen enhancement ZZ Other tickets major
#532 reggie QC wizard for additional QC measurements outside of routine new Nicklas Nordborg Request Reggie v4.x major
#584 Make it possible to use different volumes for different RNA in Create mRNA plate wizard new Nicklas Nordborg enhancement Reggie v4.x major
#585 Cluster start date shold be a date+time annotation new Nicklas Nordborg enhancement Reggie v4.x major
#586 Register end date+time for clustering new Nicklas Nordborg enhancement Reggie v4.x major
#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 Reggie v4.x major
#696 Implement some skin examples for BASE new task Skin-collection 1.0 major
#752 Schedule new RNAQC from Flagged RNA wizard new Nicklas Nordborg enhancement Reggie v4.x major
#1029 MeLuDI should be adapted to support the SCAN-B-rec project assigned olle task MeLuDI v1.6.0 major
#1126 Cohort exporter should support exporting to Excel file new enhancement Relax v1.5 major
#1146 Demux for the MIPs pipeline accepted Nicklas Nordborg task Reggie v4.23 major
#1156 Switch to Java 11 and BASE 3.15 new olle task LabEnv v1.7 major
#1159 Release exporter changes due to MIPs pipeline new Nicklas Nordborg enhancement Reggie v4.23 major
#1162 Add support for using 'M' in the read-string when demuxing new Nicklas Nordborg enhancement Reggie v4.23 major
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