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BaderLab
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EnrichmentMapApp
The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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Update App to Java 11.
#448
mikekucera
closed
3 years ago
0
DAVID/BINGO/Great import gives error "Enrichments file or GMT file is required"
#447
kjbussey
closed
3 years ago
2
Add option to colour by significant NES only
#446
risserlin
closed
3 years ago
5
Bump jackson-databind from 2.2.2 to 2.9.10.7 in /EnrichmentMapPlugin
#445
dependabot[bot]
closed
2 years ago
1
GREAT with multiple datasets: only 1 node table column containing gene set size
#444
veroniquevoisin
closed
1 year ago
4
GREAT enrichment map with multiple datasets: different number of slides in Color by Dataset or NES columns
#443
veroniquevoisin
closed
3 years ago
5
Painter app gene overlap very poor for supposedly identical pathways
#442
risserlin
closed
2 years ago
1
enrichment map from GREAT output with multiple datasets: colors don't match legend
#441
veroniquevoisin
closed
3 years ago
0
Using the Enrichment map visual style helper with generated String network doesn't work
#440
risserlin
closed
3 years ago
1
G profiler results don't import properly
#439
paraish
closed
2 years ago
4
Show in Genemania - add option to search with gene found in expression file
#438
risserlin
closed
3 years ago
1
Show in Genemania - launch from different entry points on the same selection show different menus.
#437
risserlin
closed
3 years ago
3
Compress in heatmap - all classes defined in expression and class file (irregardless of which phenotypes are being compared)
#436
risserlin
closed
3 years ago
1
latest GSEA output files not recognized by auto populate
#435
risserlin
closed
3 years ago
0
Enrichment Map JAR file Error
#434
rohitesh13
closed
3 years ago
2
Drugs Targets GeneSets not uploaded for current version
#433
keremw
closed
3 years ago
3
Latest version of GSEA (4.1.0) on Windows sets some of the p-values and FDR values to "---"
#432
risserlin
closed
3 years ago
11
Single Cell: Enrichment panel is reset (blank) after saving and reloading EM
#431
s2hui
closed
1 year ago
9
Pathways not found in GMT (even though they are there)
#430
s2hui
closed
3 years ago
1
Bump junit from 4.12 to 4.13.1 in /EnrichmentMapIntegrationTest
#429
dependabot[bot]
opened
3 years ago
0
Bump junit from 4.12 to 4.13.1 in /EnrichmentMapPlugin
#428
dependabot[bot]
opened
3 years ago
0
Show in Pathway Commons is not working
#427
s2hui
closed
1 year ago
12
Make the genes in the heatmap selectable
#426
risserlin
closed
3 years ago
0
Error while Building Enrichment Map
#425
comaxfunk
closed
3 years ago
2
EM post analysis: all nodes get selected even if only one signature gene-set is selected
#424
veroniquevoisin
closed
1 year ago
1
Filtering network should filter "color by dataset" pie slices
#423
klevdiamanti
closed
4 years ago
12
Bug in node size mapping for gs_size
#422
scaramonche
closed
4 years ago
5
Provide column with NES values in the build-table command
#421
scaramonche
closed
4 years ago
3
issue with EM sliders and post analysis on computer using French keyboard
#420
risserlin
closed
4 years ago
1
Provide numerical (gene/protein) data from columns in a network as arguments in the build-table command
#419
scaramonche
closed
4 years ago
8
Add sequential color palette to visualize q and p values on the EM network
#418
scaramonche
closed
4 years ago
8
networkName argument in build-table command
#417
scaramonche
closed
4 years ago
0
Missing argument in the build-table command to import qvalues.
#416
scaramonche
closed
4 years ago
5
Unable to create Enrichment Map: Internal Server Error Failed: null
#415
LucoLab
closed
3 years ago
3
Building GEM in Cytoscape from gProfiler .txt -->Error>"parsing generic result file"
#414
moutazhelal
closed
2 years ago
1
Bump jackson-databind from 2.2.2 to 2.9.10.4 in /EnrichmentMapPlugin
#413
dependabot[bot]
closed
3 years ago
1
Add notebook demonstrating how to use fgsea with EM
#412
risserlin
opened
4 years ago
6
EM's heatmap table Description column doesnt reflect GSEA genesets
#411
klai001
closed
4 years ago
3
Multi dataset documentation
#410
risserlin
opened
4 years ago
0
gProfiler new version support
#409
fbrundu
closed
4 years ago
2
EM3.3.0 beta2: loading files: a gene-sets (general) dataset is automatically created
#408
veroniquevoisin
closed
4 years ago
2
gmt file in edb folder is being recognized as a dataset
#407
mikekucera
closed
4 years ago
1
EM 3.3 Beta- color by dataset shows wrong colors after PA is run
#406
mikekucera
closed
4 years ago
0
EM3.3 beta: color by "all" datasets when only one or 2 datasets out of 3 are checked
#405
veroniquevoisin
closed
4 years ago
1
EM 3.3 beta - clicking on post analysis edge shows no overlap in heatmap
#404
risserlin
closed
4 years ago
0
EM 3.3 beta - load your own gmt file for signature set doesn't work
#403
risserlin
closed
4 years ago
2
mastermap command doesn't work when creating EM with just gmt files.
#402
risserlin
closed
4 years ago
0
PropertyManager needs to listen for PropertyUpdatedEvent
#401
mikekucera
closed
4 years ago
0
Bump jackson-databind from 2.2.2 to 2.9.10.3 in /EnrichmentMapPlugin
#400
dependabot[bot]
closed
4 years ago
1
Beta v3.3.0.beta1 edge heatmap empty even though there are "genes" associated with them.
#399
risserlin
closed
4 years ago
1
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