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AHBA_PFC_filtered.json
AHBA_PFC_filtered.json
 
 
Example_CellHashing_input.json
Example_CellHashing_input.json
 
 
Example_snRNA_input.json
Example_snRNA_input.json
 
 
Hybrid_subclass_markers.json
Hybrid_subclass_markers.json
 
 
PEC_scRNA_pipeline_CellBender.py
PEC_scRNA_pipeline_CellBender.py
 
 
PEC_scRNA_pipeline_CellRanger.py
PEC_scRNA_pipeline_CellRanger.py
 
 
PEC_scRNA_pipeline_Pegasus.py
PEC_scRNA_pipeline_Pegasus.py
 
 
Pegasus-Pipeline.py
Pegasus-Pipeline.py
 
 
Pegasus_spec-file.txt
Pegasus_spec-file.txt
 
 
README.md
README.md
 
 
R_spec-file.txt
R_spec-file.txt
 
 
mito_genes.csv
mito_genes.csv
 
 
run-cellbender.sh
run-cellbender.sh
 
 
run-cellranger.sh
run-cellranger.sh
 
 
run-pegasus.sh
run-pegasus.sh
 
 
slurm.template
slurm.template
 
 

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PsychENCODE_scRNA_pipeline

Documentation is provided in this link.

To clone the conda environments appropriate for running different parts of the pipeline, please use the Pegasus_spec-file.txt and R_spec-file.txt files to clone them (see instructions here).

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