BaderLab EnrichmentMapApp issues

BaderLab / 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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issues

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mastermap with commands from docker does not work

#547 risserlin opened 4 days ago
0
running enrichmentmap build command doesn't create new default visualization

#546 risserlin opened 4 days ago
1
issue installing new version of EM app if you installed through EM collection

#545 risserlin opened 1 month ago
1
No documentation discussing how to create EM from just gmt file

#544 risserlin closed 3 months ago
2
Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error"

#543 astrum1337 closed 3 months ago
3
create a subnetwork of most significant gene set per cluster

#542 veroniquevoisin closed 4 months ago
6
Input files for EnrichmentMap

#541 SchwarzLena opened 4 months ago
3
gray nodes (not colored by -log10(value)when creating the map

#540 veroniquevoisin closed 4 months ago
7
EM version 3.4.0-SNAPSHOT" Default style node color: -log10(pvalue)_max (enhancement)

#538 veroniquevoisin closed 4 months ago
8
User unaware that multi-dataset maps are supported

#537 mikekucera closed 4 months ago
1
Diffuse string Network

#536 sarneg closed 5 months ago
1
GSEA-Enrichmentmap-Cytoscape-desktop applicaion

#534 sarneg closed 3 months ago
4
If rank file starts with empty line get error

#533 risserlin closed 3 months ago
0
Different results when running via CLI vs. CyREST

#532 AlexanderPico closed 6 months ago
3
Update FilterTunables.java

#531 AlexanderPico opened 6 months ago
0
The enrichmentmap build command always creates 2 datasets when a gmt file is provided

#530 mikekucera opened 7 months ago
0
ability to layout network by dataset

#529 risserlin opened 7 months ago
0
CreateEMNetworkTask should be cancellable

#528 mikekucera closed 7 months ago
0
Building EnrichmentMap error

#527 amkhasawneh closed 9 months ago
6
filtering GSEA results by NES assumes positives are in one file and negatives are in another

#526 risserlin opened 11 months ago
3
Upgrade Java and Guice

#525 mikekucera opened 11 months ago
0
index 1 out of bounds for length 1

#524 mikekucera closed 11 months 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 9 months ago
1
Better options for controlling redundancy

#521 mikekucera closed 3 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 11 months ago
0
Use organic layout as default

#518 mikekucera closed 11 months ago
0
Style updates for EM networks

#517 mikekucera closed 9 months ago
4
Expression file with blank lines at end causes unhelpful error message.

#516 mikekucera closed 11 months 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 8 months ago
0
EM can't recover from fdr q-value of NA - infinite loop

#509 risserlin closed 8 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 8 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 8 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
Show data set colors for AutoAnnotate summary network.

#498 mikekucera closed 1 year ago
0
Bump jackson-databind from 2.2.2 to 2.13.4.1 in /EnrichmentMapPlugin

#497 dependabot[bot] closed 1 year ago
1
cytoscape Enrichment Map no responce

#496 ChaoWilliam closed 1 year ago
1