You can re-create the conda environments that was used for all these analyses with the following command:

conda create -n merck R=4.3.2
conda install --file requirements.txt

Each of the folders within this repository refers to a different dataset that was used for this correlation analysis.

1. mD_sandbox = PBMC cells sorted on celltype markers and then pooled together

2. pbmc_3k = PBMC HBC dataset used to teach scRNA

3. pbmc_multimodal = CITE-seq + RNA dataset from the Seurat azimuth celltype atlas. There are 3 folders of analyses for pbmc_multimodal dataset:

   • analysis_01 = initial look at the data as we tested best practices for correlations
   • analysis_02 = analysis of correlation outputs after running the scrna_correlation_workflow
   • analysis_03 = analysis looking at the effect of sequencing depth on the correlation results