Biowulf High Performance Computing at the NIH
bigSCale2: Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data

bigSCale is a complete framework for the analysis and visualization of single cell data. It allows to cluster, phenotype, perform pseudotime analysis, infer gene regulatory networks and reduce large datasets in smaller datasets with higher quality.


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 --mem=4g
[user@cn3316 ~]$ module load bigSCale2
[+] Loading singularity  on cn4464 
[+] Loading bigScale2 20190719  ... 
[user@cn3316 ~]$ bigSCale2
Singularity bigSCale2.sqsh:/usr/local/apps/Tybalt/0.1.3/bin>R
> library(bigSCale)
> ...
> q()
End the interactive session:
[user@cn3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$