cytoscape-helpdesk

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Welcome to the Cytoscape Helpdesk. This group is intended for discussions pertaining to the installation and operation of Cytoscape. If you are developing or maintaining your own Cytoscape app, then please consider the cytoscape-app-dev group. Questions about cytoscape.js should go to stackoverflow. Newbie questions are welcomed!

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General

If you are new to posting, following the Posting Guidelines will help you get quicker and more useful responses.

0 selected

Yogesh Gupta, Alex Pico3

Sep 17

hub taxa in network

Hi Alex, thank you so much for your reply, it seems like I need to choose lower CC and higher BC for

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hub taxa in network

Hi Alex, thank you so much for your reply, it seems like I need to choose lower CC and higher BC for

Sep 17

Pradeep Eranti, Scooter Morris2

Sep 9

How to define NA values while importing Data table?

Hi Pradeep, Well, it really depends on how you want to handle the NA values. Typically, you would

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How to define NA values while importing Data table?

Hi Pradeep, Well, it really depends on how you want to handle the NA values. Typically, you would

Sep 9

Steven Maere, Scooter Morris2

Sep 9

BiNGO 3.0.5 and PiNGO 1.5.2 released

Hi Steven, Excellent news! Thanks! -- scooter On Thursday, September 2, 2021 at 5:04:40 AM UTC-7

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BiNGO 3.0.5 and PiNGO 1.5.2 released

Hi Steven, Excellent news! Thanks! -- scooter On Thursday, September 2, 2021 at 5:04:40 AM UTC-7

Sep 9

monika chongtham, … Mike Kucera11

Sep 3

Cannot see enrichment map using the string enrichment in cytoscape

Thank you both for testing it. I'll upload version 3.3.3 of EnrichmentMap to the App Store today.

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Cannot see enrichment map using the string enrichment in cytoscape

Thank you both for testing it. I'll upload version 3.3.3 of EnrichmentMap to the App Store today.

Sep 3

Reese Hitchings

Sep 2

Identify nodes in all clusters?

Hello, I am looking for a way to output the IDs of the nodes that compose each cluster in an

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Identify nodes in all clusters?

Hello, I am looking for a way to output the IDs of the nodes that compose each cluster in an

Sep 2

sepideh...@gmail.com, … Scooter Morris6

Aug 19

ClusterMaker - Transitivity clustering doesn't work

Hi Shanthini, Can you try to run Cytoscape from the command line and send me the backtrace?

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ClusterMaker - Transitivity clustering doesn't work

Hi Shanthini, Can you try to run Cytoscape from the command line and send me the backtrace?

Aug 19

Emil Jurga, Scooter Morris2

Aug 19

using cyREST to automate annotations

Hi Emil, Annotation automation is a feature in Cytoscape 3.9, which is available as a beta. I would

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using cyREST to automate annotations

Hi Emil, Annotation automation is a feature in Cytoscape 3.9, which is available as a beta. I would

Aug 19

Cassidy Dietz, Scooter Morris3

Aug 15

Error with no report

I did. However, I have not gotten a reply :( -Cassidy On Thursday, August 12, 2021 at 5:57:39 PM UTC+

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Error with no report

I did. However, I have not gotten a reply :( -Cassidy On Thursday, August 12, 2021 at 5:57:39 PM UTC+

Aug 15

Christine P, Scooter Morris2

Aug 12

FBMN Using Cytoscape

Hi Christine, Do you see the node source in your node table? It could be that you just need to zoom

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FBMN Using Cytoscape

Hi Christine, Do you see the node source in your node table? It could be that you just need to zoom

Aug 12

Zhiliang Hu, Scooter Morris2

Aug 5

going deeper - intermediate level tutorials on syntax structure for web?

Hi Zhiliang, Sorry, this group is generally for discussing the Cytoscape desktop application.

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going deeper - intermediate level tutorials on syntax structure for web?

Hi Zhiliang, Sorry, this group is generally for discussing the Cytoscape desktop application.

Aug 5

mohana prasad, Scooter Morris4

Aug 5

MERGING NETWORK - reg

Hi Poovizhi, OK, so before the merge, you need to add a column to one of your pathways and set the

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MERGING NETWORK - reg

Hi Poovizhi, OK, so before the merge, you need to add a column to one of your pathways and set the

Aug 5

Radosław Giziński, Scooter Morris2

Aug 5

Edge draw order

Hi Radek, There is no way to control edge order in Cytoscape 3.8, but we did expose edge Z-order as a

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Edge draw order

Hi Radek, There is no way to control edge order in Cytoscape 3.8, but we did expose edge Z-order as a

Aug 5

lauren marazzi, Christopher Churas4

Aug 2

Thanks, Chris! On Monday, August 2, 2021 at 2:54:42 PM UTC-4 Chris Churas wrote: Hi, AppStore should

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Thanks, Chris! On Monday, August 2, 2021 at 2:54:42 PM UTC-4 Chris Churas wrote: Hi, AppStore should

Aug 2

Karen van Niekerk, … Karen van Niekerk3

Jul 17

Running Cytoscape 3.8.2 on Ubuntu 20.04

Thank you. It appears to help Cytoscape run more smoothly. I assumed a newer version of Java would

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Running Cytoscape 3.8.2 on Ubuntu 20.04

Thank you. It appears to help Cytoscape run more smoothly. I assumed a newer version of Java would

Jul 17

Qi Ma, Alex Pico3

Jul 16

Qi: One question for help regarding Attribute circle Layout to plot data in Cytoscape. Thank you very much.

Dear Alex, Thank you for your reply. It helps a lot. Best, Qi On Thu, Jul 15, 2021 at 9:09 AM '

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Qi: One question for help regarding Attribute circle Layout to plot data in Cytoscape. Thank you very much.

Dear Alex, Thank you for your reply. It helps a lot. Best, Qi On Thu, Jul 15, 2021 at 9:09 AM '

Jul 16

mgruzy, Christopher Churas3

Jul 9

HTTPConnectionPool when calling cyrest.cyclient()

I just checked and it seems like it needed to be updated in the app manager (just updated and it all

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HTTPConnectionPool when calling cyrest.cyclient()

I just checked and it seems like it needed to be updated in the app manager (just updated and it all

Jul 9

Leena Yadav, … Ági G11

Jul 2

error in values network files

Hi, I had the same problem as Leena. I converted .xls file into .csv file and the problem was solved.

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error in values network files

Hi, I had the same problem as Leena. I converted .xls file into .csv file and the problem was solved.

Jul 2

Christopher Churas

Jun 17

Cytoscape AppStore now redirecting all requests to https

Hi, The Cytoscape AppStore (http://apps.cytoscape.org) is now redirecting all requests to https (

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Cytoscape AppStore now redirecting all requests to https

Hi, The Cytoscape AppStore (http://apps.cytoscape.org) is now redirecting all requests to https (

Jun 17

Amin Ali, Scooter Morris2

Jun 17

Failed to map any of ?? identifiers. Mapped HGNC -> Entrez Gene

Hi Amin, You'll need to give us a bit more information. What columns do you have in your network?

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Failed to map any of ?? identifiers. Mapped HGNC -> Entrez Gene

Hi Amin, You'll need to give us a bit more information. What columns do you have in your network?

Jun 17

Yogesh Gupta, Scooter Morris6

Jun 17

Cytoscape input file preparation for hub/keystone genera identification

Hi Yogesh, If you go into the filters tab, you just click the "+" button twice and set up a

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Cytoscape input file preparation for hub/keystone genera identification

Hi Yogesh, If you go into the filters tab, you just click the "+" button twice and set up a

Jun 17

Song, Scooter Morris2

Jun 10

For Asking a question regarding edge thickness

Hi Song, The excel that you uploaded should have a column labeled "combined_score" or

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For Asking a question regarding edge thickness

Hi Song, The excel that you uploaded should have a column labeled "combined_score" or

Jun 10

RL W, Scooter Morris2

Jun 10

archived jar files in maven repository?

Ugh. Cytoscape 2.x didn't use maven at all, nor did it use OSGi or any kind of bundling. You

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archived jar files in maven repository?

Ugh. Cytoscape 2.x didn't use maven at all, nor did it use OSGi or any kind of bundling. You

Jun 10

Corry Mao, Scooter Morris2

Jun 10

after running windows.bat I still can't run cytoscape installation

Hi Corry, Can you provide us the text from your command window? -- scooter On Tuesday, June 8, 2021

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after running windows.bat I still can't run cytoscape installation

Hi Corry, Can you provide us the text from your command window? -- scooter On Tuesday, June 8, 2021

Jun 10

veronique voisin, Scooter Morris2

Jun 10

Cytoscape 3.8.2 installation issue on Mac OS BigSur 11.4 java12

Hi Veronique, Unfortunately, the troubleshooting script has an error and doesn't properly detect

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Cytoscape 3.8.2 installation issue on Mac OS BigSur 11.4 java12

Hi Veronique, Unfortunately, the troubleshooting script has an error and doesn't properly detect

Jun 10

Manoj Kumar, Scooter Morris4

Jun 10

How to run BiNGO with non-model species

That should work fine. According to the manual, you should be able to download the entire .obo file

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How to run BiNGO with non-model species

That should work fine. According to the manual, you should be able to download the entire .obo file

Jun 10

LKO, Lars Juhl Jensen2

Jun 4

string app input for immunoprecipitated data

It really comes down to what your questions are. If what you want to show is to create a network of

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string app input for immunoprecipitated data

It really comes down to what your questions are. If what you want to show is to create a network of

Jun 4

Mingxun Wang, … Dexter Pratt7

May 29

License for Cytoscape Logo

Hi Ming, GNPS looks awesome! We absolutely would like to support you in integration. Here is a

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License for Cytoscape Logo

Hi Ming, GNPS looks awesome! We absolutely would like to support you in integration. Here is a

May 29

Pranavathiyani G, … Nadezhda Doncheva4

May 29

Accessing older version of STRINGdb using Cytoscape

Thank you for the reply. In the new version of STRING DB, the reference organism strain considered

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Accessing older version of STRINGdb using Cytoscape

Thank you for the reply. In the new version of STRING DB, the reference organism strain considered

May 29

Sean, … Luis Felipe da Silva10

May 27

Unable to install - The JVM found at {0} is damaged

OMG, i love you man. Thank you so much for this. Em segunda-feira, 30 de novembro de 2015 às 17:37:14

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Unable to install - The JVM found at {0} is damaged

OMG, i love you man. Thank you so much for this. Em segunda-feira, 30 de novembro de 2015 às 17:37:14

May 27

Leila Rato, Scooter Morris7

May 27

phosphopath create new network of pathway

No, unfortunately, I don't have any other ideas. Did you try it with the sample dataset provided

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phosphopath create new network of pathway

No, unfortunately, I don't have any other ideas. Did you try it with the sample dataset provided

May 27

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