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

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Santhust, Scooter Morris2

Apr 18

scNetViz, UMAP, got 500 code from server

Hi Santhust, Sorry about that -- the service wound up on a host that wasn't configured properly.

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scNetViz, UMAP, got 500 code from server

Hi Santhust, Sorry about that -- the service wound up on a host that wasn't configured properly.

Apr 18

강민수 / 학생 / 국제농업기술학과, Alex Pico2

Apr 15

Is there a way to use edge with colored arrow with letter?

Hi. You can get pretty close, just using Edge Style mappings. See screenshot and attached CYS file….

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Is there a way to use edge with colored arrow with letter?

Hi. You can get pretty close, just using Edge Style mappings. See screenshot and attached CYS file….

Apr 15

Elena MacFarlane, Scooter Morris3

Apr 12

Cytoscape will not properly save CLUEGO files anymore (rather, it saves but will not reopen)

I could not get the support contact email from Cytoscape ClueGo page— it goes to a blank page… What

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Cytoscape will not properly save CLUEGO files anymore (rather, it saves but will not reopen)

I could not get the support contact email from Cytoscape ClueGo page— it goes to a blank page… What

Apr 12

Rishikesh Dash, … Scooter Morris4

Apr 10

How to visualize cluster graph without edges in Cytoscape

Hi Rishi, You actually don't need both source and target nodes. You can just import the source

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How to visualize cluster graph without edges in Cytoscape

Hi Rishi, You actually don't need both source and target nodes. You can just import the source

Apr 10

Pierre Klemmer, … Ronan M.T. Fleming5

Apr 8

mapTableColumn / idmapper no longer working at all

https://beta.metanetx.org/cgi-bin/mnxweb/id-mapper there is also a SPARQL endpoint. For metabolites

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mapTableColumn / idmapper no longer working at all

https://beta.metanetx.org/cgi-bin/mnxweb/id-mapper there is also a SPARQL endpoint. For metabolites

Apr 8

Barbara Darnhofer, Scooter Morris2

Apr 3

custom organism

Hi Barbara, Since this is a question specific to the ClueGO app, I would suggest reaching out to the

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custom organism

Hi Barbara, Since this is a question specific to the ClueGO app, I would suggest reaching out to the

Apr 3

Maurizio Severino, Scooter Morris2

Apr 3

raw data cytoscape

Hi Maurizio, Happy to answer some questions, but you may need to be a bit more specific. Cytoscape

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raw data cytoscape

Hi Maurizio, Happy to answer some questions, but you may need to be a bit more specific. Cytoscape

Apr 3

Mar 26

Cytoscape 3.10.2 is released!

We're very pleased to announce availability of Cytoscape 3.10.2! To get a copy, visit our

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Cytoscape 3.10.2 is released!

We're very pleased to announce availability of Cytoscape 3.10.2! To get a copy, visit our

Mar 26

Pierre Klemmer, Kristina Hanspers2

Mar 26

Creating new column in table and using it as key column for table import

Hi Pierre, For the first issue, you should be able to use SUIDs directly in R with RCy3, as the

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Creating new column in table and using it as key column for table import

Hi Pierre, For the first issue, you should be able to use SUIDs directly in R with RCy3, as the

Mar 26

Kanchan Rauthan, Scooter Morris2

Mar 20

Request to add Trichuris trichiura to cluego app

Hi Kanchan, I would reach out to the ClueGO team directly (look at the app store to get their e-mail

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Request to add Trichuris trichiura to cluego app

Hi Kanchan, I would reach out to the ClueGO team directly (look at the app store to get their e-mail

Mar 20

Firat Kurt, Scooter Morris2

Mar 20

how to enable all CPU cores in Cytoscape

By default, most multithreaded apps in Cytoscape will use all cores, but not all algorithms are

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how to enable all CPU cores in Cytoscape

By default, most multithreaded apps in Cytoscape will use all cores, but not all algorithms are

Mar 20

Kristina Hanspers2

Mar 18

Join NRNB for Google Summer of Code 2024!

The contributor application period for GSoC starts today! Application deadline is April 2 18:00 UTC.

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Join NRNB for Google Summer of Code 2024!

The contributor application period for GSoC starts today! Application deadline is April 2 18:00 UTC.

Mar 18

Ermir Zulfaj, … Ruth Isserlin5

Mar 14

Problem with building enrichment map

Hi Ermir, Please send me an example file that is not working if the below suggestion doesn't work

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Problem with building enrichment map

Hi Ermir, Please send me an example file that is not working if the below suggestion doesn't work

Mar 14

Pierre Klemmer, Ruth Isserlin2

Mar 12

Autoconfirm or deny file overwrite prompts

Hi Pierre, I have encountered this a lot. The easiest way to get around it is from R. I check if the

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Autoconfirm or deny file overwrite prompts

Hi Pierre, I have encountered this a lot. The easiest way to get around it is from R. I check if the

Mar 12

Ang Jing Jie, Scooter Morris3

Mar 10

ClueGO Startup Issue

Hi Scooter, Thanks for the suggestion. The software works well after reinstalling. Cheers, Jing On

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ClueGO Startup Issue

Hi Scooter, Thanks for the suggestion. The software works well after reinstalling. Cheers, Jing On

Mar 10

Ermir Zulfaj, Ruth Isserlin2

Mar 8

Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error"

Hi Ermir, I have never seen that error before. It is weird that you are specifying GSEA input and

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Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error"

Hi Ermir, I have never seen that error before. It is weird that you are specifying GSEA input and

Mar 8

Ben H, Scooter Morris2

Mar 7

Sorting clusters by value in column

Hi Ben, Offhand, I can't think of any easy way to do that, unfortunately. The layout shouldn'

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Sorting clusters by value in column

Hi Ben, Offhand, I can't think of any easy way to do that, unfortunately. The layout shouldn'

Mar 7

Ruth Isserlin, Alex Pico2

Mar 6

Is there a way to use the network import functions from the PSICQUIC bar as a command

Hi Ruth, That functionality is provided by this core app: https://apps.cytoscape.org/apps/

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Is there a way to use the network import functions from the PSICQUIC bar as a command

Hi Ruth, That functionality is provided by this core app: https://apps.cytoscape.org/apps/

Mar 6

Alessandra Dupont, Scooter Morris3

Feb 29

Network Randomizer stats

Hi Scooter, Thank you for the quick reply! That worked! I did not understand the order save as>

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Network Randomizer stats

Hi Scooter, Thank you for the quick reply! That worked! I did not understand the order save as>

Feb 29

Kenza Boumehdi, Scooter Morris2

Feb 28

Hi Kenza, It sounds like the Pesca Multi Shortest Paths Tree is exactly what you want. Select the

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Hi Kenza, It sounds like the Pesca Multi Shortest Paths Tree is exactly what you want. Select the

Feb 28

Adithie M, … Scooter Morris6

Feb 28

How to create subnetwork in cytoscape?

Also, make sure that you use New Network-->From Selected Nodes, All Edges. -- scooter On Thursday,

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How to create subnetwork in cytoscape?

Also, make sure that you use New Network-->From Selected Nodes, All Edges. -- scooter On Thursday,

Feb 28

Matthias König, … Valentina Cappelletti25

Feb 28

How to get Cytoscape scaled on high DPI monitor?

Works for me too! thanks a lot!! Il giorno giovedì 10 agosto 2023 alle 02:19:38 UTC+2 Scooter Morris

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using-cytoscape

How to get Cytoscape scaled on high DPI monitor?

Works for me too! thanks a lot!! Il giorno giovedì 10 agosto 2023 alle 02:19:38 UTC+2 Scooter Morris

Feb 28

MIKHAELA FRANCESCA RADAZA, … Ruth Isserlin4

Feb 26

Problems with the genes showing up

Hi Michaela, There is nothing wrong with your resulting Enrichment map. By default EM is set up to

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Problems with the genes showing up

Hi Michaela, There is nothing wrong with your resulting Enrichment map. By default EM is set up to

Feb 26

Feb 15

STRING Cytoscape Speed

They are doing different things, believe it or not. The website runs on its own hosted content while

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STRING Cytoscape Speed

They are doing different things, believe it or not. The website runs on its own hosted content while

Feb 15

John Harris, … Lars Juhl Jensen3

Feb 9

tricoloring nodes

The Omics Visualizer app is designed to do exactly what you ask for. It is built on top of

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tricoloring nodes

The Omics Visualizer app is designed to do exactly what you ask for. It is built on top of

Feb 9

Rebecca Wan, Scooter Morris4

Jan 31

Cluego- reopen cytoscape lost gene node multi-color

Hi Rebecca, OK, I've reproduced the issue, and as near as I can tell, it's a bug in ClueGO. I

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Cluego- reopen cytoscape lost gene node multi-color

Hi Rebecca, OK, I've reproduced the issue, and as near as I can tell, it's a bug in ClueGO. I

Jan 31

Rebecca Wan, Scooter Morris2

Jan 25

Cluego - multi-colors for gene nodes involved in multiple pathways

Hi Rebecca, OK, so when you open the session, the bypass values are gone. There are two possibilities

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Cluego - multi-colors for gene nodes involved in multiple pathways

Hi Rebecca, OK, so when you open the session, the bypass values are gone. There are two possibilities

Jan 25

Princy Mangla, Scooter Morris2

Jan 25

Regarding nrnb gsoc

Hi Princy, The first step would be to look at our current list of possible projects here: https://

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Regarding nrnb gsoc

Hi Princy, The first step would be to look at our current list of possible projects here: https://

Jan 25

Felipe da Veiga Leprevost, Christopher Churas4

Jan 22

PKIX path building failed

Hi, I installed linux mint 21.3 and openjdk 17.0.9 from the software manager along with Cytoscape

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PKIX path building failed

Hi, I installed linux mint 21.3 and openjdk 17.0.9 from the software manager along with Cytoscape

Jan 22

Elena MacFarlane, … Christopher Churas7

Jan 20

"Bounds" is null

Hi, Thanks for the network. Sorry about the issue, but glad you found a work around. I loaded the

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"Bounds" is null

Hi, Thanks for the network. Sorry about the issue, but glad you found a work around. I loaded the

Jan 20

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