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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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class file not working in latest EM
#550
risserlin
closed
1 week ago
6
GSEA: can't build EM with one empty report
#549
veroniquevoisin
closed
1 week ago
0
checkbox in creation dialog for running AA
#548
mikekucera
closed
1 week ago
0
mastermap with commands from docker does not work
#547
risserlin
opened
2 months ago
0
running enrichmentmap build command doesn't create new default visualization
#546
risserlin
closed
1 week ago
1
issue installing new version of EM app if you installed through EM collection
#545
risserlin
opened
3 months ago
1
No documentation discussing how to create EM from just gmt file
#544
risserlin
closed
5 months ago
2
Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error"
#543
astrum1337
closed
5 months ago
3
create a subnetwork of most significant gene set per cluster
#542
veroniquevoisin
closed
6 months ago
6
Input files for EnrichmentMap
#541
SchwarzLena
closed
1 week ago
3
gray nodes (not colored by -log10(value)when creating the map
#540
veroniquevoisin
closed
6 months ago
7
EM version 3.4.0-SNAPSHOT" Default style node color: -log10(pvalue)_max (enhancement)
#538
veroniquevoisin
closed
6 months ago
8
User unaware that multi-dataset maps are supported
#537
mikekucera
closed
6 months ago
1
Diffuse string Network
#536
sarneg
closed
7 months ago
1
GSEA-Enrichmentmap-Cytoscape-desktop applicaion
#534
sarneg
closed
5 months ago
4
If rank file starts with empty line get error
#533
risserlin
closed
5 months ago
0
Different results when running via CLI vs. CyREST
#532
AlexanderPico
closed
8 months ago
3
Update FilterTunables.java
#531
AlexanderPico
opened
8 months ago
0
The enrichmentmap build command always creates 2 datasets when a gmt file is provided
#530
mikekucera
closed
1 month ago
0
ability to layout network by dataset
#529
risserlin
opened
9 months ago
0
CreateEMNetworkTask should be cancellable
#528
mikekucera
closed
9 months ago
0
Building EnrichmentMap error
#527
amkhasawneh
closed
11 months ago
6
filtering GSEA results by NES assumes positives are in one file and negatives are in another
#526
risserlin
opened
1 year ago
3
Upgrade Java and Guice
#525
mikekucera
opened
1 year ago
0
index 1 out of bounds for length 1
#524
mikekucera
closed
1 year ago
1
Provide a sorted list of pathways
#523
mikekucera
opened
1 year ago
0
Use the node color mapping for AA clusters.
#522
mikekucera
closed
11 months ago
1
Better options for controlling redundancy
#521
mikekucera
closed
5 months ago
0
Add option to use the node with the highest significance as the label for the cluster
#520
mikekucera
closed
1 year ago
1
Automatically run AutoAnnotate when creating the EM network
#519
mikekucera
closed
1 year ago
0
Use organic layout as default
#518
mikekucera
closed
1 year ago
0
Style updates for EM networks
#517
mikekucera
closed
11 months ago
4
Expression file with blank lines at end causes unhelpful error message.
#516
mikekucera
closed
1 year ago
1
FGSEA-service: plumber rounds q-values, affects filtering
#515
mikekucera
closed
1 year ago
2
enrichmentmap build command - two generic datasets not working properly
#514
risserlin
closed
1 year ago
1
Leading edge not working in EM 3.3.5
#513
risserlin
closed
1 year ago
0
EM unable to parse directories as before in Cytoscape Beta2 3.10
#512
risserlin
opened
1 year ago
0
Error - Gene sets in enrichment file missing from GMT file
#511
lcorrie
closed
1 year ago
7
Ambiguous error message - try and create EM with just enrichments, expression and ranks but forget gmt file
#510
risserlin
closed
10 months ago
0
EM can't recover from fdr q-value of NA - infinite loop
#509
risserlin
closed
10 months ago
0
Heatmap only displaying expression/ranks for dataset where geneset is significant eventhough it is found in the second dataset
#508
risserlin
closed
10 months ago
1
Bump apache-karaf from 4.2.1 to 4.3.8 in /EnrichmentMapIntegrationTest
#507
dependabot[bot]
opened
1 year ago
0
EM 3.3.5: question? aggregated summary
#506
veroniquevoisin
closed
1 year ago
1
EM 3.3.5: force directed layout does not work on hidden edges (but organic layout does)
#505
veroniquevoisin
closed
10 months ago
2
dataset resolver doesn't work for FGSEA
#504
risserlin
closed
1 year ago
1
testing EM 3.3.5: hiding one dataset reset the style.
#503
veroniquevoisin
closed
1 year ago
2
testing EM3.3.5: changing Data Set Colors change all edges to color dataset1
#502
veroniquevoisin
closed
1 year ago
1
testing EM 3.3.5 ( enhancement): be able to see full name in heatmap table headers
#501
veroniquevoisin
closed
1 year ago
1
Is it the expectation of EM that the ranks file is sorted?
#500
risserlin
closed
1 year ago
12
Bump jackson-databind from 2.2.2 to 2.12.7.1 in /EnrichmentMapPlugin
#499
dependabot[bot]
opened
1 year ago
0
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