BEAR Applications

CellBender 0.2.0-foss-2021a-CUDA-11.3.1

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-CUDA-11.3.1

To load the module for CellBender 0.2.0-foss-2021a-CUDA-11.3.1 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load CellBender/0.2.0-foss-2021a-CUDA-11.3.1

There is a CPU version of this module: CellBender 0.2.0-foss-2021a

BEAR Apps Version

2020b

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: CUDA/11.3.1 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-CUDA-11.3.1 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, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 31st May 2022