cytoscape-helpdesk

1–30 of 4856

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!

Quick Links

Installing Cytoscape

Using Cytoscape

Apps

Cytoscape Automation

General

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

0 selected

Aug 16

Facing issue with Cluego Pedia

Hi, I tried creating networks with cluego plugin and all the pathway nodes were displayed but their

unread,

Facing issue with Cluego Pedia

Hi, I tried creating networks with cluego plugin and all the pathway nodes were displayed but their

Aug 16

Schubidu Lalala

Aug 16

nodes in alphabetical order

Hello, I create a graphic with grid layout only with nodes without edges. I want to sort the nodes

unread,

nodes in alphabetical order

Hello, I create a graphic with grid layout only with nodes without edges. I want to sort the nodes

Aug 16

Bernhard Mlecnik, Scooter Morris2

Aug 11

Cytoscape 3.9.1 problem with opening xlsx files?

Hi Bernhard, As far as I know, there's no issues with reading xlsx files. Can you tell us what

unread,

Cytoscape 3.9.1 problem with opening xlsx files?

Hi Bernhard, As far as I know, there's no issues with reading xlsx files. Can you tell us what

Aug 11

Ching Ching WEE, … Bernhard3

Aug 11

ClueGO: not able to update KEGG pathway database

Hi, yes there was a change from http to https for KEGG. We will fix this asap. Best On Monday, June

unread,

ClueGO: not able to update KEGG pathway database

Hi, yes there was a change from http to https for KEGG. We will fix this asap. Best On Monday, June

Aug 11

Amin Ali, … Scooter Morris6

Aug 9

scNetViz - loading own data

OK, can you try to download the version at: https://www.cgl.ucsf.edu/home/scooter/scNetViz-1.7.0.jar

unread,

scNetViz - loading own data

OK, can you try to download the version at: https://www.cgl.ucsf.edu/home/scooter/scNetViz-1.7.0.jar

Aug 9

Steven Blanchard, Christopher Churas4

Jul 26

Automatic move to a selected node

thank you for your reply. Le lundi 25 juillet 2022 à 18:32:39 UTC+2, Chris Churas a écrit : Hi, The

unread,

Automatic move to a selected node

thank you for your reply. Le lundi 25 juillet 2022 à 18:32:39 UTC+2, Chris Churas a écrit : Hi, The

Jul 26

clayton.curtis.md, Mike Kucera2

Jul 18

CY3D renderer question - node transparency and label visibility

I don't think so. On Sat, Jul 16, 2022 at 12:25 PM clayton.curtis.md <clayton.curtis.md@gmail.

unread,

CY3D renderer question - node transparency and label visibility

I don't think so. On Sat, Jul 16, 2022 at 12:25 PM clayton.curtis.md <clayton.curtis.md@gmail.

Jul 18

clayton.curtis.md, Mike Kucera4

Jul 18

CY3D renderer question - edge labels, label wrapping

I don't think so. On Sat, Jul 16, 2022 at 11:53 AM clayton.curtis.md <clayton.curtis.md@gmail.

unread,

CY3D renderer question - edge labels, label wrapping

I don't think so. On Sat, Jul 16, 2022 at 11:53 AM clayton.curtis.md <clayton.curtis.md@gmail.

Jul 18

clayton.curtis.md, Mike Kucera3

Jul 16

CY3D renderer question - how can the network be positioned in the CY3D network view?

The reply was indeed helpful. I'm pretty sure I would never have figured that out!! :) On Friday,

unread,

CY3D renderer question - how can the network be positioned in the CY3D network view?

The reply was indeed helpful. I'm pretty sure I would never have figured that out!! :) On Friday,

Jul 16

clayton.curtis.md, Mike Kucera3

Jul 15

CY3D style question - how to make labels visible

Thanks! Knew how to use 'select' and 'camera', but completely missed 'labels'

unread,

CY3D style question - how to make labels visible

Thanks! Knew how to use 'select' and 'camera', but completely missed 'labels'

Jul 15

Elena Navarro Carrasco, … Scooter Morris5

Jul 14

Phosphopath issue

I would suggest reaching out to the PhosphoPath authors to see if they might know what's going on

unread,

Phosphopath issue

I would suggest reaching out to the PhosphoPath authors to see if they might know what's going on

Jul 14

Mehdi Eslami, Scooter Morris2

Jul 14

initializing OSGi container ...

Wow, Mehdi. Cytoscape 3.7 is really, really old. My first suggestion would be update your Java to

unread,

initializing OSGi container ...

Wow, Mehdi. Cytoscape 3.7 is really, really old. My first suggestion would be update your Java to

Jul 14

Negar Mottaghi, Scooter Morris2

Jul 14

error opening cytoscape session file in version 3.9.1

Sorry to hear you're having problems. A good first step, particularly since your colleague can

unread,

error opening cytoscape session file in version 3.9.1

Sorry to hear you're having problems. A good first step, particularly since your colleague can

Jul 14

clayton.curtis.md, Mike Kucera3

Jul 13

How can one change the renderer being used?

Thanks for the reply!! It is very helpful. I knew how to create a CY3D view, but didn't realize

unread,

How can one change the renderer being used?

Thanks for the reply!! It is very helpful. I knew how to create a CY3D view, but didn't realize

Jul 13

Shrikirti Anand, Scooter Morris2

Jul 7

Network generation error and input file format

Hi Shrikirti, I think you're over-interpreting the "Source Node" and "Target Node

unread,

Network generation error and input file format

Hi Shrikirti, I think you're over-interpreting the "Source Node" and "Target Node

Jul 7

Ayham shakouka, Scooter Morris2

Jul 7

Finding all proteins interacting with a particular set of proteins

Greetings, I'm assuming that you are using stringApp here, since you mention confidence values,

unread,

Finding all proteins interacting with a particular set of proteins

Greetings, I'm assuming that you are using stringApp here, since you mention confidence values,

Jul 7

Tamar, Ruth Isserlin2

Jul 6

create one pathway from gene list

Hi Tamar, Which pathways are you referring to? Are your pathways in Enrichment map? (If so I can help

unread,

create one pathway from gene list

Hi Tamar, Which pathways are you referring to? Are your pathways in Enrichment map? (If so I can help

Jul 6

Simon Fox, Ruth Isserlin3

Jun 30

Enrichment map error when parsing generic results files

Hi Ruth Thanks for the reply. I did manage to work around it in the end. I think that the latest

unread,

Enrichment map error when parsing generic results files

Hi Ruth Thanks for the reply. I did manage to work around it in the end. I think that the latest

Jun 30

Ryan Podany, Scooter Morris6

Jun 23

Connecting to an external server.

Hi Ryan, Yes, you need to have a network. Going from csv to sif is actually pretty easy. The sif

unread,

Connecting to an external server.

Hi Ryan, Yes, you need to have a network. Going from csv to sif is actually pretty easy. The sif

Jun 23

Antonia Feilden, Scooter Morris2

Jun 23

windows.bat - error message - The "app" store at https://apps.cytoscape.org is not reachable

Greetings! I have a couple of questions for you that may help us figure out what might be going on:

unread,

windows.bat - error message - The "app" store at https://apps.cytoscape.org is not reachable

Greetings! I have a couple of questions for you that may help us figure out what might be going on:

Jun 23

clayton.curtis.md, Scooter Morris3

Jun 16

Unable to import styles from file

Hi Clayton, You don't see your AVIVA style in the styles menu at the top of the Styles panel? It

unread,

Unable to import styles from file

Hi Clayton, You don't see your AVIVA style in the styles menu at the top of the Styles panel? It

Jun 16

clayton.curtis.md, … Scooter Morris4

Jun 16

How can one change all of the values for a column to a single value at one time?

Hi Clayton, I agree that tab/type would typically replace. I think the reason we don't do that is

unread,

How can one change all of the values for a column to a single value at one time?

Hi Clayton, I agree that tab/type would typically replace. I think the reason we don't do that is

Jun 16

clayton.curtis.md, … Scooter Morris6

Jun 16

Is it possible to create a network by importing exported nodes and edges

Hi Clayton, I put my little app up on my web site at https://www.cgl.ucsf.edu/home/scooter/

unread,

Is it possible to create a network by importing exported nodes and edges

Hi Clayton, I put my little app up on my web site at https://www.cgl.ucsf.edu/home/scooter/

Jun 16

clayton.curtis.md, … Christopher Churas4

Jun 15

Is there a straightforward way to merge networks represented in different .cys files?

Hi, The best way to preserve styles on networks is to use the "CX JSON (.cx)" format when

unread,

Is there a straightforward way to merge networks represented in different .cys files?

Hi, The best way to preserve styles on networks is to use the "CX JSON (.cx)" format when

Jun 15

Joakim Knudsen, Scooter Morris5

Jun 10

Linear constraints on layout, allowing rotation

Thanks a lot, this is very interesting :) On Thursday, June 9, 2022 at 4:46:17 PM UTC+2 ssbsm...@

unread,

Linear constraints on layout, allowing rotation

Thanks a lot, this is very interesting :) On Thursday, June 9, 2022 at 4:46:17 PM UTC+2 ssbsm...@

Jun 10

ΠΑΡΑΣΚΕΥΗ ΜΥΛΩΝΑ, Scooter Morris2

Jun 9

Hi there, Sorry to say, but the answer is "it depends". What kind of data do you have? Do

unread,

Hi there, Sorry to say, but the answer is "it depends". What kind of data do you have? Do

Jun 9

hani sarah, … Scooter Morris8

Jun 9

Asking opinion on the right way in gene network construction

Hi Rizwan, Sara's post was from 6 years ago, can you be more specific about what species you want

unread,

Asking opinion on the right way in gene network construction

Hi Rizwan, Sara's post was from 6 years ago, can you be more specific about what species you want

Jun 9

raja sekaran, Scooter Morris2

Jun 9

Update zoom graph size by external button

Hi Rajasekaran, First, to be clear, Cytoscape 3.2.0 is *extremely* old. Using Cytoscape 3.9, pretty

unread,

Update zoom graph size by external button

Hi Rajasekaran, First, to be clear, Cytoscape 3.2.0 is *extremely* old. Using Cytoscape 3.9, pretty

Jun 9

Steven Blanchard, Alex Pico6

Jun 7

edges style and outline color

Thanks you for all your reply. I will try our advices. Steven Le lundi 6 juin 2022 à 23:28:40 UTC+2,

unread,

edges style and outline color

Thanks you for all your reply. I will try our advices. Steven Le lundi 6 juin 2022 à 23:28:40 UTC+2,

Jun 7

Søren Egstrand, Ruth Isserlin2

Jun 2

EnrichmentMap fails to start

Hi Soren, Cytoscape 3.7.1 is a pretty old version of Cytoscape. I just tried and it looks like the

unread,

EnrichmentMap fails to start

Hi Soren, Cytoscape 3.7.1 is a pretty old version of Cytoscape. I just tried and it looks like the

Jun 2

Search

Clear search

Close search

Google apps

Main menu