Biowulf High Performance Computing at the NIH
CITE-seq-Count: counting antibody TAGS from a CITE-seq and/or cell hashing experiment

CITE-seq-Count is a python package that counts antibody TAGS. It handles the data from both the Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seqi) and/or Cell Hashing experiment.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3104 ~]$ module load citeseqcount/1.4.3
[+] Loading citeseqcount 1.4.3  ...
Copy the testing scripts and data to your current folder and run the scripts:
[user@cn3104 ~]$ cp $CSCOUNT_TESTS/*.py .
[user@cn3104 ~]$ cp -r $CSCOUNT_DATA . 
[user@cn3104 ~]$ python test_io.py 
[user@cn3104 ~]$ python test_preprocessing.py    
[user@cn3104 ~]$ python test_processing.py  
Exit the application:
[user@cn3104 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$