scanpy 1.8.1-foss-2021a

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 1.8.1-foss-2021a

To load the module for scanpy 1.8.1-foss-2021a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load scanpy/1.8.1-foss-2021a

BEAR Apps Version

2021a

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

  • anndata 0.7.6
  • natsort 7.1.1
  • pynndescent 0.5.4
  • scanpy 1.8.1
  • sinfo 0.3.4
  • stdlib-list-0.8.0
  • umap-learn-0.5.1
  • xlrd 1.2.0

More Information

For more information visit the scanpy website.

Dependencies

This version of scanpy has a direct dependency on: foss/2021a h5py/3.2.1-foss-2021a leidenalg/0.8.7-foss-2021a networkx/2.5.1-foss-2021a numba/0.53.1-foss-2021a PyTables/3.6.1-foss-2021a Python/3.9.5-GCCcore-10.3.0 scikit-learn/0.24.2-foss-2021a SciPy-bundle/2021.05-foss-2021a Seaborn/0.11.2-foss-2021a statsmodels/0.12.2-foss-2021a tqdm/4.61.2-GCCcore-10.3.0

Required By

This version of scanpy is a direct dependent of: scVelo/0.2.4-foss-2021a

Last modified on 20th May 2022