BaderLab/EnrichmentMapApp

Issues

• No documentation discussing how to create EM from just gmt file

  #544 opened 3 months ago by risserlin
  2

• filtering GSEA results by NES assumes positives are in one file and negatives are in another

  #526 opened 10 months ago by risserlin
  3

• If rank file starts with empty line get error

  #533 opened 3 months ago by risserlin
  0

• Better options for controlling redundancy

  #521 opened 3 months ago by mikekucera
  0

• Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error"

  #543 opened 3 months ago by astrum1337
  3

• GSEA-Enrichmentmap-Cytoscape-desktop applicaion

  #534 opened 3 months ago by sarneg
  4

• create a subnetwork of most significant gene set per cluster

  #542 opened 3 months ago by veroniquevoisin
  6

• gray nodes (not colored by -log10(value)when creating the map

  #540 opened 3 months ago by veroniquevoisin
  7

• Input files for EnrichmentMap

  #541 opened 4 months ago by SchwarzLena
  3

• EM version 3.4.0-SNAPSHOT" Default style node color: -log10(pvalue)_max (enhancement)

  #538 opened 4 months ago by veroniquevoisin
  8

• User unaware that multi-dataset maps are supported

  #537 opened 4 months ago by mikekucera
  1

• Diffuse string Network

  #536 opened 5 months ago by sarneg
  1

• Different results when running via CLI vs. CyREST

  #532 opened 6 months ago by AlexanderPico
  3

• The enrichmentmap build command always creates 2 datasets when a gmt file is provided

  #530 opened 7 months ago by mikekucera
  0

• ability to layout network by dataset

  #529 opened 7 months ago by risserlin
  0

• CreateEMNetworkTask should be cancellable

  #528 opened 7 months ago by mikekucera
  0

• Heatmap only displaying expression/ranks for dataset where geneset is significant eventhough it is found in the second dataset

  #508 opened 7 months ago by risserlin
  1

• EM can't recover from fdr q-value of NA - infinite loop

  #509 opened 7 months ago by risserlin
  0

• Ambiguous error message - try and create EM with just enrichments, expression and ranks but forget gmt file

  #510 opened 7 months ago by risserlin
  0

• EM 3.3.5: force directed layout does not work on hidden edges (but organic layout does)

  #505 opened 8 months ago by veroniquevoisin
  2

• Building EnrichmentMap error

  #527 opened 9 months ago by amkhasawneh
  6

• Style updates for EM networks

  #517 opened 9 months ago by mikekucera
  4

• Use the node color mapping for AA clusters.

  #522 opened 9 months ago by mikekucera
  1

• Use organic layout as default

  #518 opened a year ago by mikekucera
  0

• Automatically run AutoAnnotate when creating the EM network

  #519 opened a year ago by mikekucera
  0

• Expression file with blank lines at end causes unhelpful error message.

  #516 opened a year ago by mikekucera
  1

• index 1 out of bounds for length 1

  #524 opened a year ago by mikekucera
  1

• Upgrade Java and Guice

  #525 opened a year ago by mikekucera
  0

• Provide a sorted list of pathways

  #523 opened a year ago by mikekucera
  0

• Add option to use the node with the highest significance as the label for the cluster

  #520 opened a year ago by mikekucera
  1

• enrichmentmap build command - two generic datasets not working properly

  #514 opened a year ago by risserlin
  1

• FGSEA-service: plumber rounds q-values, affects filtering

  #515 opened a year ago by mikekucera
  2

• Leading edge not working in EM 3.3.5

  #513 opened a year ago by risserlin
  0

• EM unable to parse directories as before in Cytoscape Beta2 3.10

  #512 opened a year ago by risserlin
  0

• Error - Gene sets in enrichment file missing from GMT file

  #511 opened a year ago by lcorrie
  7

• testing EM3.3.5: changing Data Set Colors change all edges to color dataset1

  #502 opened 2 years ago by veroniquevoisin
  1

• testing EM 3.3.5: hiding one dataset reset the style.

  #503 opened 2 years ago by veroniquevoisin
  2

• testing EM 3.3.5 ( enhancement): be able to see full name in heatmap table headers

  #501 opened 2 years ago by veroniquevoisin
  1

• EM 3.3.5: question? aggregated summary

  #506 opened 2 years ago by veroniquevoisin
  1

• dataset resolver doesn't work for FGSEA

  #504 opened 2 years ago by risserlin
  1

• Is it the expectation of EM that the ranks file is sorted?

  #500 opened 2 years ago by risserlin
  12

• Mastermap with enrichmentmap of Great results: gs_size should be changed to be TotalGenes instead of ObsGenes TotalGenes

  #495 opened 2 years ago by veroniquevoisin
  6

• enhancement RCy3: enrichmentmap build with Great: not able to filter using binomial q value (only hypergeometric test available)

  #494 opened 2 years ago by veroniquevoisin
  1

• Show data set colors for AutoAnnotate summary network.

  #498 opened 2 years ago by mikekucera
  0

• g:profiler not running

  #489 opened 2 years ago by risserlin
  11

• cytoscape Enrichment Map no responce

  #496 opened 2 years ago by ChaoWilliam
  1

• Add ability to create subnetwork from visible nodes.

  #493 opened 2 years ago by mikekucera
  1

• question or enhancement: gene set signature cut-off:can't filter less than 0.001 or 0.0001

  #491 opened 2 years ago by veroniquevoisin
  0

• Issue using enrichment map columns in Cytoscape formula builder

  #492 opened 2 years ago by risserlin
  3

• July gene sets (at least the Human ones) are missing the genes

  #490 opened 2 years ago by toddajohnson
  2