PavlidisLab Gemma issues

PavlidisLab / Gemma

Genomics data re-analysis

Apache License 2.0

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issues

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Show bioassay sparsity metrics in the diagnostic tab

#1295 arteymix opened 3 days ago
0
Automation of "subset" tag

#1294 xnrxng opened 4 days ago
5
Differential expression with single cell data

#1293 arteymix opened 5 days ago
0
Tag subsets with a copy of the factor value's characteristics when subsetting

#1292 arteymix opened 1 week ago
0
eBayes fails on dataset

#1291 ppavlidis opened 1 week ago
0
Make selection of arbitirary baselines for DEA deterministic and/or add more rules.

#1290 ppavlidis opened 1 week ago
6
Replace JAWR with Webpack

#1289 arteymix closed 1 week ago
0
UI work for single-cell

#1288 arteymix closed 1 week ago
1
Filter cells to be included in a pseudo-bulk

#1287 arteymix opened 2 weeks ago
0
Add HANCESTRO and AFPO to the basic set of ontologies

#1286 arteymix closed 4 days ago
2
Provide auto-completion for enumerated options

#1285 arteymix opened 3 weeks ago
0
Restore/improve support for non-GEO dataset upload (esp. single-cell)

#1284 ppavlidis opened 3 weeks ago
1
Show pubpeer plugin results on experiment pages with publications

#1283 ppavlidis opened 3 weeks ago
3
Dataset searches from home page yielding a single experiment should navigate directly there

#1282 ppavlidis opened 3 weeks ago
0
Support writing data matrices with target scale type without generating new vectors

#1281 arteymix opened 3 weeks ago
3
Always generate a count QT if possible

#1280 arteymix opened 3 weeks ago
2
Filter which subsets are retained when generating pseudo-bulks

#1279 arteymix opened 3 weeks ago
0
Support non-integer counting data

#1278 arteymix closed 1 week ago
0
Expose EE subsets in the REST API

#1277 arteymix opened 3 weeks ago
0
Support log-transformed counting data

#1276 arteymix closed 1 week ago
2
Update maven-site-plugin to 3.21

#1275 arteymix opened 3 weeks ago
1
Deal with log-transformed sparse data

#1274 arteymix closed 3 weeks ago
1
Keep track of the number of cells with at least one expressed gene in samples and pseudo-bulks

#1273 arteymix opened 4 weeks ago
4
Use 200 instead of "default" as a response code in docs

#1272 arteymix opened 4 weeks ago
0
Add a `/datasets/{dataset}/quantitationTypes/{quantitationType}` endpoint

#1271 arteymix opened 4 weeks ago
0
User interface requirements for single-cell

#1270 arteymix opened 1 month ago
1
Fill missing feature type when converting legacy genes.tsv.gz to features.tsv.gz

#1269 arteymix opened 1 month ago
0
Generate data histograms to help determine the scale type

#1268 arteymix opened 1 month ago
0
Error when using splitExperiment CLI for GSE123919

#1267 SalvaSherif2532 opened 1 month ago
0
Include single-cell characteristics to the EE2C table

#1266 arteymix opened 1 month ago
0
Add single-cell fields to the search index

#1265 arteymix opened 1 month ago
0
CLI tool for aggregating single cell data

#1264 arteymix closed 3 weeks ago
6
Provide HTML preview for TGEMO terms

#1263 arteymix opened 1 month ago
1
Quick Go To Experiment/Platform/Gene/etc. page when using Explore > Browse > Go with an unambiguous identifier

#1262 arteymix opened 1 month ago
0
NullPointerException when accessing GSE193022

#1261 arteymix closed 1 month ago
1
Cookie “SPRING_SECURITY_REMEMBER_ME_COOKIE” rejected because it has the “SameSite=None” attribute but is missing the “secure” attribute.

#1260 arteymix opened 1 month ago
1
Label datasets with an "assay" term automatically

#1259 arteymix opened 1 month ago
0
Predicate filtering

#1258 xnrxng opened 1 month ago
1
Ontology index files are getting closed

#1257 arteymix closed 1 month ago
3
Drop Gemma Groovy Support

#1256 arteymix opened 1 month ago
1
Provide shell completion for loggers and log levels with -v and --logger options

#1255 arteymix opened 1 month ago
0
Allow serving already gzipped filed via the REST API

#1254 arteymix closed 1 month ago
0
Addressing author-provided batch info

#1253 alexmillett20 opened 1 month ago
2
Indicate the original design element in single cell data vectors

#1252 arteymix closed 1 month ago
1
Replace probe with element in the REST API terminology

#1251 arteymix opened 1 month ago
0
Modernize URLs

#1250 arteymix opened 1 month ago
1
Add a mechanism when writing data files to mark them as ready

#1249 arteymix opened 1 month ago
2
Add CLIs and tools for writing MEX files

#1248 arteymix closed 1 month ago
3
Matrix writer for single cell data

#1247 arteymix closed 1 month ago
1
PubMed tests randomly fail with 400 errors on the CI

#1246 arteymix closed 1 month ago
2