Question

Is there a way to easily export a .mtx file from a seurat object and use it in the scNetViz app for Cytoscape?

0

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2.5 years ago

Ondina ▴ 100

Hello everyone,

I have a question. I want to use the scNetViz app that can be used in Cytoscape. It's an app that allows the user to generate networks from single-cell data which is quite interesting. The problem is that it uses the raw matrix.mtx data so the clusters that will be analysed are the clusters generated automatically with Cellranger. So I was wondering if there's a way to convert the data from Seurat, so the new clusters associated with the gene ids, into an .mtx file which is compatible with scNetViz?

conversion cytoscape singlecell format seurat • 1.6k views

ADD COMMENT • link updated 2.5 years ago by scooter ▴ 620 • written 2.5 years ago by Ondina ▴ 100

1

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I cannot comment on Seurat but in general any numeric matrix can be saved as mtx via Matrix::writeMM().

ADD REPLY • link 2.5 years ago by ATpoint 86k

score 3 · Accepted Answer · 2022-06-16

scNetViz uses .mtx files by default. You should be able to do an Apps->scNetViz->Load Experiment->From file and point it to a directory containing the .mtx file and the two header files. Then it should just import. Make sure to set the species -- you'll need to have the correct species to generate your networks. Let me know if you have problems!

-- scooter