BEAR Applications

scvi-tools 0.20.1-foss-2022a

scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

Accessing scvi-tools 0.20.1-foss-2022a

To load the module for scvi-tools 0.20.1-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load scvi-tools/0.20.1-foss-2022a

There is a GPU enabled version of this module: scvi-tools 0.20.1-foss-2022a-CUDA-11.7.0

BEAR Apps Version

2022a

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

• cached-property-1.5.2
• chex 0.1.6
• contextlib2 21.6.0
• docrep 0.3.2
• flax 0.6.4
• ml_collections 0.1.1
• mudata 0.2.1
• multipledispatch 0.6.0
• numpyro 0.11.0
• optax 0.1.4
• orbax 0.1.2
• pyro-api-0.1.2
• pyro-ppl-1.8.4
• scvi_tools 0.20.1
• tensorstore 0.1.32
• toolz 0.12.0

More Information

For more information visit the scvi-tools website.

Dependencies

This version of scvi-tools has a direct dependency on: dm-tree/0.1.8-GCCcore-11.3.0 foss/2022a h5py/3.7.0-foss-2022a IPython/8.5.0-GCCcore-11.3.0 jax/0.4.4-foss-2022a matplotlib/3.5.2-foss-2022a openpyxl/3.0.10-GCCcore-11.3.0 poetry/1.2.2-GCCcore-11.3.0 Python/3.10.4-GCCcore-11.3.0 PyTorch-Lightning/1.9.3-foss-2022a scanpy/1.9.1-foss-2022a scikit-learn/1.1.2-foss-2022a scikit-misc/0.1.4-foss-2022a SciPy-bundle/2022.05-foss-2022a

Required By

This version of scvi-tools is a direct dependent of: cell2location/0.1.3-foss-2022a

Other Versions

These versions of scvi-tools 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 27th February 2023