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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Dec 6

FYI: The Zulu port of OpenJDK for ARM64 does not work with Cytoscape's installer

The installer for Cytoscape (Install4j) crashes on new M1 Macs with the Zulu port of OpenJDK for

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FYI: The Zulu port of OpenJDK for ARM64 does not work with Cytoscape's installer

The installer for Cytoscape (Install4j) crashes on new M1 Macs with the Zulu port of OpenJDK for

Dec 6

Purrsia Felidae, Scooter Morris3

Dec 2

How to size and color nodes by source and target columns separately

Hi Scooter, First, thank you so very much for such a clear response on what to do . The import worked

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How to size and color nodes by source and target columns separately

Hi Scooter, First, thank you so very much for such a clear response on what to do . The import worked

Dec 2

Cinmoyee Baruah, … Scooter Morris4

Dec 2

Problem with saving a network image

Hi Cinmoyee, OK, so I think the problem you are seeing is that the exported image is a full

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Problem with saving a network image

Hi Cinmoyee, OK, so I think the problem you are seeing is that the exported image is a full

Dec 2

Elvira Inglese, … Elena MacFarlane29

Dec 2

show gene after cluego analysis

Hi! Thank you for your reply— I was actually able to see where it goes eventually—the file is created

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show gene after cluego analysis

Hi! Thank you for your reply— I was actually able to see where it goes eventually—the file is created

Dec 2

German Rosano, Scooter Morris2

Dec 2

Decimals in node table from Excel file

Greetings! Well, I've never seen that before. Are you importing directly as an Excel spreadsheet,

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Decimals in node table from Excel file

Greetings! Well, I've never seen that before. Are you importing directly as an Excel spreadsheet,

Dec 2

Caitlin Gibbons, Scooter Morris2

Dec 2

Help with PPI network construction, diffeentially expressed genes, and using cytoHubba (total beginner).

Hi Caitlin, Well, at the risk of taking away the fun you'll have figuring this out yourself (

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Help with PPI network construction, diffeentially expressed genes, and using cytoHubba (total beginner).

Hi Caitlin, Well, at the risk of taking away the fun you'll have figuring this out yourself (

Dec 2

Dariel, … iris kreft9

Dec 1

removing duplicate edges

Hi, you can use R to remove duplicated values cor_matrix_melt = cor_matrix_melt[!duplicated(

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removing duplicate edges

Hi, you can use R to remove duplicated values cor_matrix_melt = cor_matrix_melt[!duplicated(

Dec 1

Keionn Lai, Scooter Morris2

Nov 18

bundling edges failed for cytoscape network (string and intact combined)

Hi Keionn, Yes, unfortunately, Bundle Edges is extremely inefficient and is due to be replace in 3.10

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bundling edges failed for cytoscape network (string and intact combined)

Hi Keionn, Yes, unfortunately, Bundle Edges is extremely inefficient and is due to be replace in 3.10

Nov 18

Nov 18

cytoscape 2.8.2 errors upon launch

Hello all, I am very new to cytoscape, which i need to use for my thesis and specifically i need this

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cytoscape 2.8.2 errors upon launch

Hello all, I am very new to cytoscape, which i need to use for my thesis and specifically i need this

Nov 18

Mema Stamataki, … Scooter Morris5

Nov 18

Cytoscape 2.8.2 Installation Problems

Well, Cytoscape 2.8 definitely won't run on Java 17. If memory serves (and this was a *long* time

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Cytoscape 2.8.2 Installation Problems

Well, Cytoscape 2.8 definitely won't run on Java 17. If memory serves (and this was a *long* time

Nov 18

Drishtee Barua, Alex Pico2

Nov 11

Regarding Bundling of large-sized networks

Ah, you've found one of the most inefficient functions in all of Cytoscape! Seriously, "

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Regarding Bundling of large-sized networks

Ah, you've found one of the most inefficient functions in all of Cytoscape! Seriously, "

Nov 11

Mema Stamataki, Alex Pico2

Nov 11

Illegal reflective access

Answered on Stackoverflow: https://stackoverflow.com/questions/69890828/cytoscape-2-8-2-launch-with-

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Illegal reflective access

Answered on Stackoverflow: https://stackoverflow.com/questions/69890828/cytoscape-2-8-2-launch-with-

Nov 11

Gilles Marodon2

Nov 4

PB installation CS 3.9.0 on Ubuntu 20.04

I reinstall Java and everything works fine now. Please disregerd my post. Thanks and apologies Le

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PB installation CS 3.9.0 on Ubuntu 20.04

I reinstall Java and everything works fine now. Please disregerd my post. Thanks and apologies Le

Nov 4

Francesca Sacco, Scooter Morris2

Nov 4

Cytoscape 3.8, 3.8.2, 3.9 do not start

Hi Francesca, According to the backtrace, you seem to be running Java 8, not Java 11. What do you see

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Cytoscape 3.8, 3.8.2, 3.9 do not start

Hi Francesca, According to the backtrace, you seem to be running Java 8, not Java 11. What do you see

Nov 4

Jordan Langston, Scooter Morris3

Nov 4

Thank you! On Thursday, November 4, 2021 at 11:18:46 AM UTC-4 ssbsm...@gmail.com wrote: Cytoscape

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Thank you! On Thursday, November 4, 2021 at 11:18:46 AM UTC-4 ssbsm...@gmail.com wrote: Cytoscape

Nov 4

Amin Ali, Scooter Morris2

Nov 4

scNetViz - loading own data

Hi Amin, Take a look at Use Case #2 in the paper: https://f1000research.com/articles/10-448 That

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scNetViz - loading own data

Hi Amin, Take a look at Use Case #2 in the paper: https://f1000research.com/articles/10-448 That

Nov 4

Michel Michaels, Scooter Morris2

Nov 4

Display selected edge with linked nodes only

Hi Michel, 1) Use the filters tab and create a column filter for the edge attribute you are

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Display selected edge with linked nodes only

Hi Michel, 1) Use the filters tab and create a column filter for the edge attribute you are

Nov 4

Gavin Lu, Scooter Morris3

Oct 28

Cytoscape interface resized after open cytocape web browser

Thanks a lot ! problem solved. On Thursday, October 28, 2021 at 8:18:10 AM UTC-7 ssbsm...@gmail.com

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Cytoscape interface resized after open cytocape web browser

Thanks a lot ! problem solved. On Thursday, October 28, 2021 at 8:18:10 AM UTC-7 ssbsm...@gmail.com

Oct 28

Cinmoyee Baruah, Scooter Morris2

Oct 28

Large network creation

Greetings, I assume you are using the "bundle edges" option in the Layout menu. With a

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Large network creation

Greetings, I assume you are using the "bundle edges" option in the Layout menu. With a

Oct 28

Oct 21

Cytoscape 3.9.0 is released!

Cytoscape 3.9.0 is released! =+=+ =+=+ =+=+ =+=+ =+=+ Hello Cytoscapers =+=+ =+=+ =+=+ =+=+ =+=+ We

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Cytoscape 3.9.0 is released!

Cytoscape 3.9.0 is released! =+=+ =+=+ =+=+ =+=+ =+=+ Hello Cytoscapers =+=+ =+=+ =+=+ =+=+ =+=+ We

Oct 21

Ruth Isserlin, Alex Pico3

Oct 19

Difference between command run using RCy3 and using command line in cytoscape

Hi Alex, Thanks! Swapping the quotes fixed the issue. Ruth On Mon, Oct 18, 2021 at 9:30 PM 'Alex

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Difference between command run using RCy3 and using command line in cytoscape

Hi Alex, Thanks! Swapping the quotes fixed the issue. Ruth On Mon, Oct 18, 2021 at 9:30 PM 'Alex

Oct 19

Keqiang An, Scooter Morris2

Oct 14

Extraction of ego etworks

Greetings, You don't mention how you are extracting the first neighbors, but if you are using the

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Extraction of ego etworks

Greetings, You don't mention how you are extracting the first neighbors, but if you are using the

Oct 14

indrani biswas, Scooter Morris2

Oct 7

cytoscape use for network generation

Cytoscape itself doesn't have a built-in database of interactions. You would need to find a

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cytoscape use for network generation

Cytoscape itself doesn't have a built-in database of interactions. You would need to find a

Oct 7

monika chongtham, … Scooter Morris13

Oct 7

Cannot see enrichment map using the string enrichment in cytoscape

You should be able to change things by using the Style Tab in left-hand panel. Node Fill Color and

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Cannot see enrichment map using the string enrichment in cytoscape

You should be able to change things by using the Style Tab in left-hand panel. Node Fill Color and

Oct 7

Daniela Janeva, Dexter Pratt2

Oct 5

Networks visualization

Try the Copycat layout app https://apps.cytoscape.org/apps/copycatlayout On Monday, October 4, 2021

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Networks visualization

Try the Copycat layout app https://apps.cytoscape.org/apps/copycatlayout On Monday, October 4, 2021

Oct 5

Pavan Baichan, Alex Pico2

Oct 1

Clustering and visulisation formatting

Hi Pavan, We have tutorials for just this sort of things at http://tutorials.cytoscape.org/. Search

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Clustering and visulisation formatting

Hi Pavan, We have tutorials for just this sort of things at http://tutorials.cytoscape.org/. Search

Oct 1

Yogesh Gupta, Chris Churas2

Sep 30

how change thickness of edges in network based on correlation value

Hi, Maybe I'm misunderstanding this, but it seems like you could set a continuous mapping on the

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how change thickness of edges in network based on correlation value

Hi, Maybe I'm misunderstanding this, but it seems like you could set a continuous mapping on the

Sep 30

Sep 25

Visualisation of StringApp clustering

Resolved. Thank you. On Friday, 24 September 2021 at 20:12:42 UTC+2 Pavan Baichan wrote: Good day, I

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Visualisation of StringApp clustering

Resolved. Thank you. On Friday, 24 September 2021 at 20:12:42 UTC+2 Pavan Baichan wrote: Good day, I

Sep 25

Reese Hitchings, Chris Churas2

Sep 23

Identify nodes in all clusters?

Hi, You could try clustermaker2 which has a bunch of clustering algorithms: https://apps.cytoscape.

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Identify nodes in all clusters?

Hi, You could try clustermaker2 which has a bunch of clustering algorithms: https://apps.cytoscape.

Sep 23

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

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