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.
-
mD_sandbox= PBMC cells sorted on celltype markers and then pooled together -
pbmc_3k= PBMC HBC dataset used to teach scRNA -
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