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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Brandon Tylke, Christopher Churas3

Dec 5

https://nrnb-nexus.ucsd.edu/ Certificate Expired

Hi, Fixed now. Sorry about that. chris On Thu, Dec 5, 2024 at 5:51 AM Brandon Tylke <btylke@

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https://nrnb-nexus.ucsd.edu/ Certificate Expired

Hi, Fixed now. Sorry about that. chris On Thu, Dec 5, 2024 at 5:51 AM Brandon Tylke <btylke@

Dec 5

HFazel, … Nadezhda Doncheva30

Nov 26

string-db data load error

Hi Carmen, Unfortunately, as of 30th Oct 2024, stringApp no longer has access to STRING v11.5. If you

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string-db data load error

Hi Carmen, Unfortunately, as of 30th Oct 2024, stringApp no longer has access to STRING v11.5. If you

Nov 26

Hayat Mohammed, Scooter Morris4

Nov 21

Yes, I found it a bit complicated also. I don't use ClueGO much, so maybe others on the list can

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Yes, I found it a bit complicated also. I don't use ClueGO much, so maybe others on the list can

Nov 21

Saad Khan, Scooter Morris2

Nov 21

Unable to make enhanced graphics work for circos

OK, I was able to get this to work. I think the problem is that your sender_celltype and

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Unable to make enhanced graphics work for circos

OK, I was able to get this to work. I think the problem is that your sender_celltype and

Nov 21

Kapil, Alex Pico2

Nov 20

Regarding installation of cytohubba

If you launch Cytoscape first and then go to https://apps.cytoscape.org/apps/cytohubba, you will see

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Regarding installation of cytohubba

If you launch Cytoscape first and then go to https://apps.cytoscape.org/apps/cytohubba, you will see

Nov 20

Wall Net, Scooter Morris2

Nov 13

Unable to update GO

I believe that's covered in the clueGO documentation, although I've heard reports that

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Unable to update GO

I believe that's covered in the clueGO documentation, although I've heard reports that

Nov 13

Guntaas Shergill, Scooter Morris2

Nov 13

Requesting help with Edge Weighted Graph Creation (Cytoscape)

Greetings Guntaas, Well, 20000 nodes is quite a lot for a simulation. I've done some testing and

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Requesting help with Edge Weighted Graph Creation (Cytoscape)

Greetings Guntaas, Well, 20000 nodes is quite a lot for a simulation. I've done some testing and

Nov 13

HK, Ruth Isserlin3

Nov 11

Question on Cytoscape for RNAseq

Also, given your type of data if you are also looking for differential pathways as well and not just

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Question on Cytoscape for RNAseq

Also, given your type of data if you are also looking for differential pathways as well and not just

Nov 11

Oct 24

Cytoscape 3.10.3 is released!

We're very pleased to announce availability of Cytoscape 3.10.3! To get a copy, visit our

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Cytoscape 3.10.3 is released!

We're very pleased to announce availability of Cytoscape 3.10.3! To get a copy, visit our

Oct 24

Col Studillo, … Scooter Morris3

Oct 16

Error in painting structures in Chemviz

Hi There, I'm the ChemViz2 author -- have you downloaded the latest version? I thought I had

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Error in painting structures in Chemviz

Hi There, I'm the ChemViz2 author -- have you downloaded the latest version? I thought I had

Oct 16

ishita jaiswal, Kristina Hanspers2

Oct 14

Introduction and Enquiry on Contributing to NRNB for GSOC 2025

Hi Ishita, Thank you for your interest in NRNB. GSoC 2024 just completed and we will not start

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Introduction and Enquiry on Contributing to NRNB for GSOC 2025

Hi Ishita, Thank you for your interest in NRNB. GSoC 2024 just completed and we will not start

Oct 14

Matthew GREFF, Ruth Isserlin2

Oct 1

nooby needs help

HI Mathew, You can map your values in the style to X position, y position and z position. Ruth From:

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nooby needs help

HI Mathew, You can map your values in the style to X position, y position and z position. Ruth From:

Oct 1

Alexandra Ioana Moatar, … Mike Kucera5

Sep 18

Error in building Enrichment Map Index 0 out of bounds for length 0

Thank you very much! I installed the latest version of Enrichment Map and I didn't get the error

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Error in building Enrichment Map Index 0 out of bounds for length 0

Thank you very much! I installed the latest version of Enrichment Map and I didn't get the error

Sep 18

Fletcher Barton, … Alex Pico4

Sep 17

We switched to manual moderation a while back. Every post is moderated UNLESS the author has

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We switched to manual moderation a while back. Every post is moderated UNLESS the author has

Sep 17

Balasubramaniam Namasivayam, … Ruth Isserlin8

Aug 30

Shortcuts for layout

Hi Ruth, Many thanks for your email. I just run the command and it does work the way I intended. This

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Shortcuts for layout

Hi Ruth, Many thanks for your email. I just run the command and it does work the way I intended. This

Aug 30

Anusha Patodia, Scooter Morris2

Aug 14

cytohubba issue

Hi Anusha, It's working for me. What version of Cytoscape and what OS are you using? If you run

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cytohubba issue

Hi Anusha, It's working for me. What version of Cytoscape and what OS are you using? If you run

Aug 14

VAIDIK BHARDWAJ, Kristina Hanspers2

Aug 8

Hi Vaidik, Thank you for your interest in NRNB. For Cytoscape, there is a nice guide for how to get

unread,

Hi Vaidik, Thank you for your interest in NRNB. For Cytoscape, there is a nice guide for how to get

Aug 8

Jan Baumann, … Scooter Morris13

Aug 7

Cytoscape stuck at "finalize" when opening session file

Hi Nafiz, Yes, when you delete your CytoscapeConfiguration directory, you also delete all of the

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Cytoscape stuck at "finalize" when opening session file

Hi Nafiz, Yes, when you delete your CytoscapeConfiguration directory, you also delete all of the

Aug 7

Petar Donchev, … Alex Pico3

Aug 1

Gene Set Enrichment analysis problem

Hi Petar. If you post this question at the PathVisio repo, then the right folks will see it and

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Gene Set Enrichment analysis problem

Hi Petar. If you post this question at the PathVisio repo, then the right folks will see it and

Aug 1

Marwan Haioun, … Nadezhda Doncheva3

Aug 1

stringApp functional enrichment

Hi Marwan, Regarding the export of tables, it is indeed already on the list of features, we just have

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stringApp functional enrichment

Hi Marwan, Regarding the export of tables, it is indeed already on the list of features, we just have

Aug 1

Nabil Asyraf, Scooter Morris2

Jul 31

A newbie question- importing data from table

Hi Nabil, At this point, there's no way to have more than one label on an edge, although you can

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A newbie question- importing data from table

Hi Nabil, At this point, there's no way to have more than one label on an edge, although you can

Jul 31

Daniel Mulholland, Ruth Isserlin2

Jul 29

Figure legend for passthrough mapping

In the style tab in the menu in the top right of the panel one of the options is to create a legend.

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Figure legend for passthrough mapping

In the style tab in the menu in the top right of the panel one of the options is to create a legend.

Jul 29

Daniel Mulholland, Ruth Isserlin2

Jul 29

Copy pasting a set of numbers from one column to another

Hi Daniel, I am not sure if a direct copy and paste command will work into the column of a table. I

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Copy pasting a set of numbers from one column to another

Hi Daniel, I am not sure if a direct copy and paste command will work into the column of a table. I

Jul 29

Naveen prasath, Scooter Morris2

Jul 25

CLUEGO VISUALIZATION

Hi Naveen, Your going to have to be a bit more specific. What are your nodes and edges? What is the

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CLUEGO VISUALIZATION

Hi Naveen, Your going to have to be a bit more specific. What are your nodes and edges? What is the

Jul 25

CD, Scooter Morris2

Jul 18

Demo link does not load

Hi there, In general, this forum is for the desktop version of Cytoscape. You would probably have

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Demo link does not load

Hi there, In general, this forum is for the desktop version of Cytoscape. You would probably have

Jul 18

yasemin ekinci, Scooter Morris4

Jul 18

According to the ClueGO documentation: ClueGO provides predefined selection criteria of

unread,

According to the ClueGO documentation: ClueGO provides predefined selection criteria of

Jul 18

yasemin ekinci, … Alex Pico3

Jul 11

Clue Go : not able to update

I'll just add that we have also had difficulty reaching the app authors. Apologies for the

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Clue Go : not able to update

I'll just add that we have also had difficulty reaching the app authors. Apologies for the

Jul 11

Ulrike Resch, Ruth Isserlin3

Jul 11

Metascape-network-output

Dear Ruth, thank you so much for the fast and competent reply- works! :-) ad question 2:- export: i

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Metascape-network-output

Dear Ruth, thank you so much for the fast and competent reply- works! :-) ad question 2:- export: i

Jul 11

mahima srinivasan, Ruth Isserlin2

Jul 10

Genemania filtering of network

How large of a genemania network are you working with? Are you pulling in gene related to your query

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Genemania filtering of network

How large of a genemania network are you working with? Are you pulling in gene related to your query

Jul 10

Alex Abdun-Nabi, … Christopher Churas6

Jul 1

Directional Selection in GUI?

Hi, Sorry if this was answered already, or if I have misread the question, but to select first

unread,

Directional Selection in GUI?

Hi, Sorry if this was answered already, or if I have misread the question, but to select first

Jul 1

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