PavlidisLab/Gemma

Issues

• Data truncation: Data too long for column 'NAME' at row 1 when analyzing GSE152294

  #1219 opened 19 days ago by arteymix
  1

• Support reading cell IDs from MEX datasets with cells.tsv.gz

  #1213 opened a month ago by arteymix
  1

• Assign cells to coarse cell types when creating pseudo-bulks

  #1216 opened 20 days ago by arteymix
  0

• Other cell-level factors to consider and their implication on subsetting

  #1218 opened 19 days ago by arteymix
  0

• Better provision for submitter-supplied batch information (avoid overwrite by Gemma-generated)

  #1217 opened 19 days ago by ppavlidis
  0

• NullPointerException in ExpressionExperimentController.loadExpressionExperimentDetails() DWR call

  #1215 opened 22 days ago by arteymix
  0

• DWR exceptions are not logged server-side

  #1206 opened a month ago by arteymix
  1

• Handle MEX datasets with barcode_metadata.tsv.gz files

  #1210 opened a month ago by arteymix
  1

• Read NCBI API key from NCBI_API_KEY

  #1212 opened a month ago by arteymix
  0

• Invalid character found in the request target for a URL apparently coming from GemBrow

  #1214 opened a month ago by arteymix
  0

• Support ZIP archive lookup for MEX files

  #1211 opened a month ago by arteymix
  2

• Restrict genes by platforms when searching them in the experiment page

  #1207 opened a month ago by arteymix
  3

• Add arguments to listGEOData to match other experiment-oriented CLIs

  #1209 opened a month ago by arteymix
  2

• Ignore small experiments when splitting on import

  #1208 opened a month ago by arteymix
  0

• NoSuchElementException when writing an analysis result set to disk

  #1205 opened a month ago by arteymix
  2

• Negative `in` operator for filters

  #1192 opened 2 months ago by arteymix
  1

• FactorValueValue objects are not fully populated for experimentalFactors for getDatasetDifferentialExpressionAnalyses endpoint

  #1201 opened 2 months ago by oganm
  7

• ontology service thread cancellation kills CLI tools that use ontologies

  #1203 opened 2 months ago by ppavlidis
  0

• Breaking changes for 2.9.0

  #1198 opened 2 months ago by arteymix
  2

• Dataset on blacklisted platform managed to get loaded

  #1200 opened 2 months ago by ppavlidis
  0

• Error marshalling java.lang.Long: Format error converting XXXXX

  #1199 opened 2 months ago by arteymix
  0

• Factor values can be duplicated when populating a continuous factor

  #1185 opened 3 months ago by arteymix
  1

• No adapter for handler [ubic.gemma.web.controller.coexpressionSearch.CoexpressionSearchController@10e181e8]: The DispatcherServlet configuration needs to include a HandlerAdapter that supports this handler

  #1169 opened 2 months ago by arteymix
  0

• /datasets/analyses/differential/results/genes/{gene} fails on staging

  #1179 opened 2 months ago by oganm
  10

• /annotations/search endpoint returns incorrect results

  #1195 opened 2 months ago by oganm
  1

• Cannot delete or update a parent row: a foreign k ey constraint fails (`gemd`.`BIO_MATERIAL_FACTOR_VALUES`, CONSTRAINT `BIO_MATERIAL_FACTOR_VALUES_FKC` FOREIGN KEY (`FACTOR_VALUES_FK`) REFERENCES `FACTOR_VALUE` (`ID`))

  #1167 opened 2 months ago by arteymix
  0

• IllegalArgumentException: Cannot pass vectors from more than one quantitation type: QuantitationType Id=532865 Name=VALUE - Processed version General Type=QUANTITATIVE Type=AMOUNT Scale=LOG2 Representation=DOUBLE [Normalized] [Preferred] vs QuantitationType Id=532864 Name=VALUE - Processed version General Type=QUANTITATIVE Type=AMOUNT Scale=LOG2 Representation=DOUBLE [Normalized] [Preferred]

  #1177 opened 3 months ago by arteymix
  1

• commons-lang3 RandomUtils has gotten very slow

  #1194 opened 2 months ago by arteymix
  1

• Increase minimum Maven version to 3.6.3

  #1193 opened 2 months ago by arteymix
  0

• Cannot delete or update a parent row: a foreign key constraint fails (`gemd`.`EXPERIMENTS2EXPRESSION_EXPERIMENT_SETS`, CONSTRAINT `FKBC3597A89FCB738D` FOREIGN KEY (`EXPERIMENTS_FK`) REFERENCES `INVESTIGATION` (`ID`))

  #1166 opened 2 months ago by arteymix
  1

• Explore samples in Gemma via the REST API

  #1191 opened 2 months ago by arteymix
  0

• An unhandled exception was intercepted: NullPointerException:

  #1170 opened 2 months ago by arteymix
  0

• NullPointerException when loading data for GSE229915

  #1190 opened 2 months ago by arteymix
  1

• Counts by technology type do not sum up to the total number of datasets

  #1188 opened 2 months ago by arteymix
  3

• Missing retainedTermUris parameter in query

  #1178 opened 2 months ago by arteymix
  0

• Genes cannot be search by any GO term

  #1187 opened 2 months ago by arteymix
  2

• Gemma browser error: invalid request for anotations/children endpoint

  #1189 opened 2 months ago by ppavlidis
  1

• GemmaAndExperimentalFactorOntologyTest is timing out on the CI

  #1186 opened 2 months ago by arteymix
  0

• Increase rendering resolution of diagnostic plots

  #1184 opened 3 months ago by arteymix
  0

• UI components for single-cell

  #1183 opened 3 months ago by arteymix
  0

• `/expressionExperiment/showExpressionExperimentSubSet.html` needs some attention

  #1182 opened 3 months ago by arteymix
  0

• ExpressionExperimentBatchCorrectionServiceTest.testComBatOnEE fails on the CI

  #1181 opened 3 months ago by arteymix
  3

• java.lang.IllegalArgumentException: All vectors must belong to ExpressionExperiment Id=36760 Name=Molecular and cellular alterations associated with long-term murine mammary cancer prevention following short-ter m tamoxifen chemoprevention indicate luminal progenitor cells as targets Short Name=GSE43809

  #1174 opened 3 months ago by arteymix
  0

• Fix colour scale for continuous factors in heatmap visualisation

  #1180 opened 3 months ago by ppavlidis
  0

• Use subsets as collection of cell populations bioassays

  #1175 opened 3 months ago by arteymix
  0

• Remove usages of SimpleFormController

  #1172 opened 3 months ago by arteymix
  0

• Redirection from / to /home.html does not preserve query parameters

  #1171 opened 3 months ago by arteymix
  1

• Result sets can be split over multiple pages in the getResultSets() endpoint

  #1168 opened 3 months ago by arteymix
  1

• Include baselines (and interaction baselines) in `getDatasetsDifferentialExpressionAnalysisResultsByGene`

  #1164 opened 3 months ago by arteymix
  1

• Endpoints returning resultSets failing to return all results

  #1162 opened 3 months ago by oganm
  3