scCODA 0.1.8-foss-2021b

scCODA allows for identification of compositional changes in high-throughput sequencing count data, especially cell compositions from scRNA-seq. It also provides a framework for integration of cell-type annotated data directly from scanpy and other sources. Aside from the scCODA model (B├╝ttner, Ostner et al (2021)), the package also allows the easy application of other differential testing methods.

Accessing scCODA 0.1.8-foss-2021b

To load the module for scCODA 0.1.8-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load scCODA/0.1.8-foss-2021b

BEAR Apps Version

2021b

Architectures

EL8-cascadelakeEL8-haswellEL8-icelake

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.

Extensions

  • scCODA 0.1.8

More Information

For more information visit the scCODA website.

Dependencies

This version of scCODA has a direct dependency on: ArviZ/0.11.4-foss-2021b foss/2021b matplotlib/3.4.3-foss-2021b Python/3.9.6-GCCcore-11.2.0 rpy2/3.4.5-foss-2021b scanpy/1.8.2-foss-2021b scikit-bio/0.5.7-foss-2021b scikit-learn/1.0.1-foss-2021b Seaborn/0.11.2-foss-2021b statsmodels/0.13.1-foss-2021b TensorFlow/2.8.4-foss-2021b tensorflow-probability/0.16.0-foss-2021b

Last modified on 2nd December 2022