TumorDecon 1.1.1-foss-2020b

TumorDecon 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 and BEAR Cloud VMs):

📋 module load TumorDecon/1.1.1-foss-2020b

BEAR Apps Version

2020b

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used 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.

Extensions

• combat 0.3.2
• dill 0.3.6
• multiprocess 0.70.14
• singscore 0.1
• TumorDecon 1.1.1
• wget 3.2

More Information

For more information visit the TumorDecon website.

Dependencies

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