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

Hello @vrbana

You can use SCNIC to do these between data type correlations. To do this I am just allowing the user to use Spearman, Pearson or Kendall-Wright correlation and making a network and correlations file so nothing too fancy. I have not implemented this functionality in q2-SCNIC at this point and have plans to in the future but it won’t be in the next month. If you want to use it in SCNIC then you can export the biom tables from your .qza's and then use those with SCNIC_analysis.py between.

Mike

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Sounds great, thanks! I’ll give it a try outside of q2

Dear Michael,

I’m trying to install the q2-SCNIC plug in with qiime2-2018.11, but I got the following error:

Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

  • q2-phylogeny=2018.11.0
  • q2-quality-control=2018.11.0
  • q2-scnic
  • r-snow=0.4_3
    Use "conda info " to see the dependencies for each package.

What I’m doing is, within the activate env, the following command:

conda config --add channels bioconda
conda config --add channels conda-forge
conda install -c conda-forge blas=1.1
conda install -c lozuponelab q2-SCNIC

Is there anything I can do to fix it?
I still have it working in a qiime2-2018.8 env, so not a big deal at the moment but I let you know about this just in case.
Best,
Luca

Hey there @llenzi! I will let @michael.shaffer reply to this, but in the meantime, I took a look at the q2-SCNIC recipe (I am not a developer of this plugin), and it looks like the recipe indicates that it is only compatible with 2018.8 (at least as far as conda is concerned). There is probably no real reason for that, maybe @michael.shaffer can update the recipe to indicate 2018.8 as a minimum version. Anyway, until you hear back from @michael.shaffer, I would suggest just continuing with your 2018.8 env, no worries about having more than one QIIME 2 env on a machine. :t_rex:

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Wow, thanks for bringing us such a nice tool. I will certainlly give it a try as soon as I can!

Hello @llenzi,

@thermokarst is right. I will be pushing out a big update to q2-SCNIC that will come out hopefully in the next week or two that will include an update to the qiime 2 base version. For now I’d recommend continuing to use q2-SCNIC in your 2018.8 environment.

Mike

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An off-topic reply has been split into a new topic: Can’t run q2-SCNIC

Please keep replies on-topic in the future.

q2-SCNIC has now been updated for 2018.11. An additional feature update will be released soon.

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An off-topic reply has been split into a new topic: Q2-scnic packagenotfounderror

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An off-topic reply has been split into a new topic: Issues with q2-scnic

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An off-topic reply has been split into a new topic: Plugin error from SCNIC: No p or p_adj in correls

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

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A post was split to a new topic: Can’t install q2-SCNIC

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.

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,

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

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

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

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Hi @kohei-108 ,

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

Best Regards,
Madhawa

An off-topic reply has been split into a new topic: I am wondering How you import the biom file including the (spp or the genus level) as my .biom file contains only the sequence representing every OTU

Please keep replies on-topic in the future.