Documentation for CIBERSORTx Input Generation

[Souhatifour]

Issue:
Here are the steps to generate input files for CIBERSORTx when using single-cell reference data.

1. Set RUN_CIBERSORT_GENES to = True in the second part of the tutorial. This will writes out CIBERSORTx input files (e.g., all-synovium_0_cybersort_sig.tsv)

2. Upload Single-Cell Reference File:

   • Navigate to https://cibersortx.stanford.edu/upload.php.
   • Create an account
   • Upload a file similar to ** "all-synovium_0_cybersort_sig.tsv** (generated from step 1)
   • This file is a single-cell reference file.

3. Create Signature Matrix File:

   • Go to https://cibersortx.stanford.edu/runcibersortx.php.
   • Select the the uploaded file in step 2.
   • Choose "custom" and select "scRNA-seq."
   • Use default parameters.
   • The generated signature matrix file will be named like "CIBERSORTx_Job23_all-
     synovium_0_cybersort_sig_inferred_phenoclasses.CIBERSORTx_Job23_all-
     synovium_0_cybersort_sig_inferred_refsample.bm.K999."

4. Deconvolution and Comparison with BuDDI:

   • Utilize the generated signature matrix file for deconvolution.
   • The resulting file for comparison with BuDDI will resemble "CIBERSORTx_Job20_all-
     liver_0_cybersort_sig_inferred_phenoclasses."