BEAR Applications

CellBender 0.2.0-foss-2021a

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Accessing CellBender 0.2.0-foss-2021a

To load the module for CellBender 0.2.0-foss-2021a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load CellBender/0.2.0-foss-2021a

There is a GPU enabled version of this module: CellBender 0.2.0-foss-2021a-CUDA-11.3.1

BEAR Apps Version

2021a

Architectures

EL8-cascadelake — EL8-haswell — EL8-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

• anndata 0.8.0
• CellBender 0.2.0
• natsort 8.1.0
• opt_einsum 3.3.0
• pyro-api-0.1.2
• pyro-ppl-1.7.0
• sphinx-argparse-0.3.1
• sphinx_autodoc_typehints 1.15.1
• sphinx_rtd_theme 1.0.0
• sphinxcontrib-programoutput-0.17

More Information

For more information visit the CellBender website.

Dependencies

This version of CellBender has a direct dependency on: foss/2021a h5py/3.2.1-foss-2021a matplotlib/3.4.2-foss-2021a PyTables/3.6.1-foss-2021a Python/3.9.5-GCCcore-10.3.0 PyTorch/1.10.0-foss-2021a scikit-learn/0.24.2-foss-2021a tqdm/4.61.2-GCCcore-10.3.0

Other Versions

These versions of CellBender are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 31st May 2022