TumorDecon 1.1.1-foss-2020bTumorDecon software includes four deconvolution methods (DeconRNAseq [Gong2013], CIBERSORT [Newman2015], ssGSEA [Şenbabaoğlu2016], Singscore [Foroutan2018]) and several signature matrices of various cell types, including LM22. The input of this software is the gene expression profile of the tumor, and the output is the relative number of each cell type.
Accessing TumorDecon 1.1.1-foss-2020b
To load the module for TumorDecon 1.1.1-foss-2020b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load TumorDecon/1.1.1-foss-2020b
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.
- combat 0.3.2
- dill 0.3.6
- multiprocess 0.70.14
- singscore 0.1
- TumorDecon 1.1.1
- wget 3.2
For more information visit the TumorDecon website.
This version of TumorDecon has a direct dependency on: BeautifulSoup/4.9.3-GCCcore-10.2.0 foss/2020b matplotlib/3.3.3-foss-2020b Python/3.8.6-GCCcore-10.2.0 scikit-learn/0.23.2-foss-2020b SciPy-bundle/2020.11-foss-2020b Seaborn/0.11.1-foss-2020b statsmodels/0.12.1-foss-2020b
Last modified on 25th November 2022