q2-SCNIC: A tool for making correlation networks, finding modules of observations and summarizing them

[didietkeren (Didit)]

Hi, when will be any updates on q2-scnic for the latest qiime2 version? Thanks

[cquin]

Hello, I am following the q2-SCNIC pipeline in QIIME2 core- 2018.8 and am on the "Calculating correlations and making your network" step.
Everytime I try to run qiime SCNIC calculate-correlations --i-table test-filtered.qza --p-method sparcc --o-correlation-table fake_correls.qza
I get an error saying:
Plugin error from SCNIC:
[Errno 2] No such file or directory: 'fastspar'
Debug info has been saved to /tmp/qiime2-q2cli-err-iy4g0idr.log

Things I have tried: reinstalling everything:

conda install -c conda-forge blas=1.1
conda update -n base -c defaults conda
conda install -c lozuponelab q2-SCNIC
pip install scnic
conda install fastspar
conda update fastspar
At some point I also tried,
conda config --add channels conda-forge
conda config --add channels defaults
Nothing worked. I then tried running Spearman correlation thinking it was just an issue with fastspar and I got:
Plugin error from SCNIC:
calculate_correlations() got an unexpected keyword argument 'p_adjustment_method'
Debug info has been saved to /tmp/qiime2-q2cli-err-xd2b8aj_.log

So I think it's an issue with my SCNIC.
Any feedback would be greatly appreciated.

[arwqiime (ARW)]

I was following your instructions to add q2-SCNIC to q2-2021.2
conda install -c conda-forge blas=1.1
It causes a downgrade of blas; is this necessary, or should it be avoided?

The following packages will be DOWNGRADED:
blas 2.17-openblas → 1.1-openblas

Best,

[mneranjan31 (Madhawa Gunathilake)]

Dear All,

I am trying to use q2-SCNIC to generate the correlation network using the genus level table in my microbiome data. I have generated ‘network-module.qza’ file which could be imported to cytoscape according to the tutorial. I am wondering whether is it possible to directly import a .qza format network file to cytoscape for the visualization? If it is not possible import directly, could you please suggest me a possible way to import the ‘module-network.qza’ file generated by q2-SCNIC to cytoscape? Any help is greatly appreciated!

Thanks in advance!
Madhawa

[mohsen_ej (Mohsen)]

thank you for your great tutorial. but how we can identify hub nodes in qiime2 if we don't want to use WGCNA?

[kohei-108 (Kohei Ito)]

Hello @mneranjan31

You can use qiime tools extract command.

Exporting a feature table

# The directory that you’re extracting to must already exist.
mkdir extracted-network/
qiime tools extract --input-path network-module.qza --output-path extracted-network/

Then, you can find network.gml in extracted-network/{random string}/data/.

You load this file into Cytoscape.

Kohei

[mneranjan31 (Madhawa Gunathilake)]

Hi @kohei-108 ,

Thank you for your kind help with the command. It is very helpful for me.!!

Best Regards,
Madhawa