Code to analyze Perturb-multiome experiments

This repository contains custom code to analyze Perturb-multiome experiments. Below, you can find the title of the corresponding notebook or script in this GitHub repository next to a brief explanation of its purpose.

1. GITHUB_processing_RNA_object: first notebook to process the output from Cellranger.
   
   
2. GITHUB_processing_perturb_multiome_object: second notebook to prepare the single cell object. The final single cell object is obtained in 3a
   
   
3. TF_sensitive_element_computation
   -3a. GITHUB_TF_sensitive_element_computation: contains code to obtain the final single cell object and perform the first step of TF-sensitive element computation
   
   -3b. mixscale_script_only_final_step_for_Terra_WDL.R. This can be run using terra.bio using the WDL script from step 3c
   
   -3c. WDL: WDL code to run the prior script, 3b, as a workflow in terra.bio. You need to update /path/to/mixscale_script_only_final_step_for_Terra_WDL.R to the bucket path where you place that script
   
   
4. GITHUB_RNA_ATAC_WNN_UMAPs: contains code to generate WNN UMAPs
   
   
5. figR_script_by_target.R: script to compute correlations
   
   
6. GITHUB_RNA_ATAC_correlations: imports correlations from figR for downstream analyses
   
   
7. GITHUB_generating_QC_plots: to generate QC metric plots
   
   
8. LDSC folder, contains the following files:
   -8a. GITHUB_LD_regression_first_step
   -8b. GITHUB_LD_regression_second_step
   -8c. WDL_LDSC: the WDL used to run the final step of LDSC regression on genomic features of choice, as referenced in 8a or 8b.
   
   
9. GITHUB_Scavenge: contains code to run Scavenge analyses.
   

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