scanpy 1.9.1-foss-2022a

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Accessing scanpy 1.9.1-foss-2022a

To load the module for scanpy 1.9.1-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load scanpy/1.9.1-foss-2022a

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

  • anndata 0.8.0
  • natsort 8.2.0
  • scanpy 1.9.1
  • session_info 1.0.0
  • sinfo 0.3.4
  • stdlib-list-0.8.0
  • xlrd 2.0.1

More Information

For more information visit the scanpy website.

Dependencies

This version of scanpy has a direct dependency on: foss/2022a h5py/3.7.0-foss-2022a leidenalg/0.9.1-foss-2022a networkx/2.8.4-foss-2022a numba/0.56.4-foss-2022a PyTables/3.8.0-foss-2022a Python/3.10.4-GCCcore-11.3.0 scikit-learn/1.1.2-foss-2022a SciPy-bundle/2022.05-foss-2022a Seaborn/0.12.1-foss-2022a statsmodels/0.13.1-foss-2022a tqdm/4.64.0-GCCcore-11.3.0 umap-learn/0.5.3-foss-2022a

Required By

This version of scanpy is a direct dependent of: cell2location/0.1.3-foss-2022a-CUDA-11.7.0 cell2location/0.1.3-foss-2022a scvi-tools/0.20.1-foss-2022a-CUDA-11.7.0 scvi-tools/0.20.1-foss-2022a

Other Versions

These versions of scanpy 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