Documentation for CIBERSORTx Input Generation

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."