SoupX 1.4.8-foss-2019b-R-3.6.2Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018)
Accessing SoupX 1.4.8-foss-2019b-R-3.6.2
To load the module for SoupX 1.4.8-foss-2019b-R-3.6.2 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load SoupX/1.4.8-foss-2019b-R-3.6.2
BEAR Apps Version
EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
- SoupX 1.4.8
For more information visit the SoupX website.
This version of SoupX has a direct dependency on: foss/2019b R/3.6.2-foss-2019b Seurat/3.2.0-foss-2019b-R-3.6.2
Last modified on 13th November 2020