Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / baderlab/enrichmentmapapp issues and pull requests

#551 - Merge Tool to visualise communalities between two networks

Issue - State: open - Opened by LilliThePink 2 months ago - 2 comments

#550 - class file not working in latest EM

Issue - State: closed - Opened by risserlin 3 months ago - 6 comments

#549 - GSEA: can't build EM with one empty report

Issue - State: closed - Opened by veroniquevoisin 4 months ago

#548 - checkbox in creation dialog for running AA

Issue - State: closed - Opened by mikekucera 4 months ago

#548 - checkbox in creation dialog for running AA

Issue - State: closed - Opened by mikekucera 4 months ago

#547 - mastermap with commands from docker does not work

Issue - State: open - Opened by risserlin 5 months ago
Labels: bug

#547 - mastermap with commands from docker does not work

Issue - State: open - Opened by risserlin 5 months ago
Labels: bug

#546 - running enrichmentmap build command doesn't create new default visualization

Issue - State: closed - Opened by risserlin 5 months ago - 1 comment
Labels: enhancement

#544 - No documentation discussing how to create EM from just gmt file

Issue - State: closed - Opened by risserlin 8 months ago - 2 comments

#544 - No documentation discussing how to create EM from just gmt file

Issue - State: closed - Opened by risserlin 8 months ago - 2 comments

#542 - create a subnetwork of most significant gene set per cluster

Issue - State: closed - Opened by veroniquevoisin 9 months ago - 6 comments

#542 - create a subnetwork of most significant gene set per cluster

Issue - State: closed - Opened by veroniquevoisin 9 months ago - 6 comments

#541 - Input files for EnrichmentMap

Issue - State: closed - Opened by SchwarzLena 9 months ago - 3 comments

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

Issue - State: closed - Opened by veroniquevoisin 9 months ago - 7 comments

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

Issue - State: closed - Opened by veroniquevoisin 9 months ago - 7 comments

#537 - User unaware that multi-dataset maps are supported

Issue - State: closed - Opened by mikekucera 10 months ago - 1 comment

#537 - User unaware that multi-dataset maps are supported

Issue - State: closed - Opened by mikekucera 10 months ago - 1 comment

#536 - Diffuse string Network

Issue - State: closed - Opened by sarneg 10 months ago - 1 comment

#536 - Diffuse string Network

Issue - State: closed - Opened by sarneg 10 months ago - 1 comment

#534 - GSEA-Enrichmentmap-Cytoscape-desktop applicaion

Issue - State: closed - Opened by sarneg 10 months ago - 4 comments

#534 - GSEA-Enrichmentmap-Cytoscape-desktop applicaion

Issue - State: closed - Opened by sarneg 10 months ago - 4 comments

#533 - If rank file starts with empty line get error

Issue - State: closed - Opened by risserlin 10 months ago
Labels: bug

#533 - If rank file starts with empty line get error

Issue - State: closed - Opened by risserlin 10 months ago
Labels: bug

#532 - Different results when running via CLI vs. CyREST

Issue - State: closed - Opened by AlexanderPico 11 months ago - 3 comments

#532 - Different results when running via CLI vs. CyREST

Issue - State: closed - Opened by AlexanderPico 11 months ago - 3 comments

#531 - Update FilterTunables.java

Pull Request - State: open - Opened by AlexanderPico 11 months ago

#531 - Update FilterTunables.java

Pull Request - State: open - Opened by AlexanderPico 11 months ago

#529 - ability to layout network by dataset

Issue - State: open - Opened by risserlin 12 months ago
Labels: enhancement

#529 - ability to layout network by dataset

Issue - State: open - Opened by risserlin 12 months ago
Labels: enhancement

#528 - CreateEMNetworkTask should be cancellable

Issue - State: closed - Opened by mikekucera 12 months ago

#528 - CreateEMNetworkTask should be cancellable

Issue - State: closed - Opened by mikekucera 12 months ago

#527 - Building EnrichmentMap error

Issue - State: closed - Opened by amkhasawneh about 1 year ago - 6 comments

#527 - Building EnrichmentMap error

Issue - State: closed - Opened by amkhasawneh about 1 year ago - 6 comments

#526 - filtering GSEA results by NES assumes positives are in one file and negatives are in another

Issue - State: closed - Opened by risserlin over 1 year ago - 3 comments
Labels: bug

#525 - Upgrade Java and Guice

Issue - State: open - Opened by mikekucera over 1 year ago

#525 - Upgrade Java and Guice

Issue - State: open - Opened by mikekucera over 1 year ago

#524 - index 1 out of bounds for length 1

Issue - State: closed - Opened by mikekucera over 1 year ago - 1 comment

#524 - index 1 out of bounds for length 1

Issue - State: closed - Opened by mikekucera over 1 year ago - 1 comment

#523 - Provide a sorted list of pathways

Issue - State: open - Opened by mikekucera over 1 year ago

#523 - Provide a sorted list of pathways

Issue - State: open - Opened by mikekucera over 1 year ago

#522 - Use the node color mapping for AA clusters.

Issue - State: closed - Opened by mikekucera over 1 year ago - 1 comment

#522 - Use the node color mapping for AA clusters.

Issue - State: closed - Opened by mikekucera over 1 year ago - 1 comment

#521 - Better options for controlling redundancy

Issue - State: closed - Opened by mikekucera over 1 year ago

#521 - Better options for controlling redundancy

Issue - State: closed - Opened by mikekucera over 1 year ago

#518 - Use organic layout as default

Issue - State: closed - Opened by mikekucera over 1 year ago

#518 - Use organic layout as default

Issue - State: closed - Opened by mikekucera over 1 year ago

#517 - Style updates for EM networks

Issue - State: closed - Opened by mikekucera over 1 year ago - 4 comments

#517 - Style updates for EM networks

Issue - State: closed - Opened by mikekucera over 1 year ago - 4 comments

#516 - Expression file with blank lines at end causes unhelpful error message.

Issue - State: closed - Opened by mikekucera over 1 year ago - 1 comment

#516 - Expression file with blank lines at end causes unhelpful error message.

Issue - State: closed - Opened by mikekucera over 1 year ago - 1 comment

#515 - FGSEA-service: plumber rounds q-values, affects filtering

Issue - State: closed - Opened by mikekucera over 1 year ago - 2 comments
Labels: question

#515 - FGSEA-service: plumber rounds q-values, affects filtering

Issue - State: closed - Opened by mikekucera over 1 year ago - 2 comments
Labels: question

#514 - enrichmentmap build command - two generic datasets not working properly

Issue - State: closed - Opened by risserlin over 1 year ago - 1 comment
Labels: bug

#514 - enrichmentmap build command - two generic datasets not working properly

Issue - State: closed - Opened by risserlin over 1 year ago - 1 comment
Labels: bug

#513 - Leading edge not working in EM 3.3.5

Issue - State: closed - Opened by risserlin over 1 year ago
Labels: bug

#513 - Leading edge not working in EM 3.3.5

Issue - State: closed - Opened by risserlin over 1 year ago
Labels: bug

#511 - Error - Gene sets in enrichment file missing from GMT file

Issue - State: closed - Opened by lcorrie almost 2 years ago - 7 comments

#511 - Error - Gene sets in enrichment file missing from GMT file

Issue - State: closed - Opened by lcorrie almost 2 years ago - 7 comments

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

Issue - State: closed - Opened by risserlin almost 2 years ago
Labels: bug

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

Issue - State: closed - Opened by risserlin almost 2 years ago
Labels: bug

#507 - Bump apache-karaf from 4.2.1 to 4.3.8 in /EnrichmentMapIntegrationTest

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#507 - Bump apache-karaf from 4.2.1 to 4.3.8 in /EnrichmentMapIntegrationTest

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#506 - EM 3.3.5: question? aggregated summary

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 1 comment

#506 - EM 3.3.5: question? aggregated summary

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 1 comment

#504 - dataset resolver doesn't work for FGSEA

Issue - State: closed - Opened by risserlin almost 2 years ago - 1 comment

#504 - dataset resolver doesn't work for FGSEA

Issue - State: closed - Opened by risserlin almost 2 years ago - 1 comment

#503 - testing EM 3.3.5: hiding one dataset reset the style.

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 2 comments

#503 - testing EM 3.3.5: hiding one dataset reset the style.

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 2 comments

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

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 1 comment
Labels: enhancement

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

Issue - State: closed - Opened by veroniquevoisin almost 2 years ago - 1 comment
Labels: enhancement

#500 - Is it the expectation of EM that the ranks file is sorted?

Issue - State: closed - Opened by risserlin almost 2 years ago - 12 comments
Labels: question

#500 - Is it the expectation of EM that the ranks file is sorted?

Issue - State: closed - Opened by risserlin almost 2 years ago - 12 comments
Labels: question

#499 - Bump jackson-databind from 2.2.2 to 2.12.7.1 in /EnrichmentMapPlugin

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#499 - Bump jackson-databind from 2.2.2 to 2.12.7.1 in /EnrichmentMapPlugin

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#498 - Show data set colors for AutoAnnotate summary network.

Issue - State: closed - Opened by mikekucera about 2 years ago
Labels: enhancement

#498 - Show data set colors for AutoAnnotate summary network.

Issue - State: closed - Opened by mikekucera about 2 years ago
Labels: enhancement

#497 - Bump jackson-databind from 2.2.2 to 2.13.4.1 in /EnrichmentMapPlugin

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies