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CytoSig is a data-driven infrastructure hosted by the National Cancer Institute. CytoSig includes both a database of target genes modulated by cytokines and a predictive model of cytokine signaling activity and regulatory cascade from transcriptomic profiles.

References:

• Peng Jiang, Yu Zhang, Beibei Ru, Yuan Yang, Trang Vu, Rohit Pau, Amer Mirza, Grégoire Altan-Bonnet, Lingrui Liu, Eytan Ruppin, Lalage Wakefield and Kai W. Wucherpfennig,
  Systematic investigation of cytokine signaling activity at the tissue and single-cell levels
  Nature Methods 2021, VOL. 18 1181–1191.

• CytoSig Home Page
• CytoSig Github page

• Module Name: CytoSig (see the modules page for more information)
• Unusual environment variables set
  • CYTOSIG_HOME  installation directory
  • CYTOSIG_BIN       executable directory
  • CYTOSIG_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=8g -c8 --gres=lscratch:10
[user@cig 3335 ~]$ module load CytoSig
[+] Loading singularity  3.10.5  on cn3335
[+] Loading CytoSig  0.1
[user@cn3335 ~]$ CytoSig_run.py -h
Usage:
CytoSig_run.py -i <input profiles> -o <output prefix> -r <randomization count, default: 1000> -a <penalty alpha, default: 10000> -e <generate excel report: 0|1, default: 0> -s <use an expanded response signature: 0|1, default: 0>

Download the CytoSig repository with test data to the current folder:

[user@cn3335 ~]$ wget https://github.com/data2intelligence/CytoSig/archive/refs/tags/v0.1.tar.gz
[user@cn3335 ~]$ tar -zxf v0.1.tar.gz & rm -f v0.1.tar.gz
[user@cn3335 ~]$ cd CytoSig-0.1

Run the unit test:

[user@cn3335 ~]$ python3-cs -m unittest tests.prediction
Output:
 Use permutation test with nrand = 1000
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Use permutation test with nrand = 1000
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----------------------------------------------------------------------
Ran 1 test in 3.095s

OK

Run SitoSig on test data:

[user@cn3335 ~]$ CytoSig_run.py -i CytoSig-0.1/tests/GSE147507.diff.gz  -o output 
Use permutation test with nrand = 1000
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