scNetViz - loading own data

Amin Ali

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Oct 28, 2021, 7:16:03 PM10/28/21

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Hi there,

I was wondering if there a step to step instruction on how to load my own data into scNetViz? I'm really looking forward in trying to analyse my data on cytoscape.

Thanks in advance,

Amin

Scooter Morris

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Nov 4, 2021, 11:24:44 AM11/4/21

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Hi Amin,

Take a look at Use Case #2 in the paper: https://f1000research.com/articles/10-448 That contains step-by-step instructions for loading your own data.

-- scooter

Elena MacFarlane

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Aug 4, 2022, 2:52:33 PM8/4/22

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Hello, for some reason, while I am able to load data from the Atlas, when I click on Load experiment--> import from in the sequence below, nothing happens. No browser window opens for me to select a folder or file.

Choose Apps → scNetViz → Load Experiment → Import from file from the menu, then browse to locate and open a zip, tar.gz, tgz, or gzip file of the three MatrixMarket files (.mtx, .mtx_cols, .mtx_rows) comprising a normalized scRNA-seq quantification dataset.

I cannot find any help on this issue anywhere, seems like it is only happening to me?

Thank you!

Elena

Screen Shot 2022-08-04 at 2.48.51 PM.png

Scooter Morris

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Aug 9, 2022, 11:38:12 AM8/9/22

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Hi Elena,

Can you tell us what version of scNetViz you are running? Version 1.7 fixed a number of issues with loading experiments from file. Also, what type of computer are you using?

-- scooter

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Elena MacFarlane

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Aug 9, 2022, 11:43:15 AM8/9/22

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Thank you-

ScNetViz is 1.7 and my mac is MacBook Pro i7– attached photos with details

Sent from my iPhone

On Aug 9, 2022, at 11:38 AM, Scooter Morris <ssbsm...@gmail.com> wrote:

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Scooter Morris

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Aug 9, 2022, 11:52:44 AM8/9/22

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

Thanks!

-- scooter

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