scanpy 1.8.2-foss-2021b

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 1.8.2-foss-2021b

To load the module for scanpy 1.8.2-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load scanpy/1.8.2-foss-2021b

BEAR Apps Version

2021b

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 0.7.8
  • natsort 8.0.2
  • pynndescent 0.5.5
  • scanpy 1.8.2
  • sinfo 0.3.4
  • stdlib-list-0.8.0
  • umap-learn-0.5.2
  • xlrd 1.2.0

More Information

For more information visit the scanpy website.

Dependencies

This version of scanpy has a direct dependency on: foss/2021b h5py/3.6.0-foss-2021b leidenalg/0.8.8-foss-2021b networkx/2.6.3-foss-2021b numba/0.54.1-foss-2021b PyTables/3.6.1-foss-2021b Python/3.9.6-GCCcore-11.2.0 scikit-learn/1.0.1-foss-2021b SciPy-bundle/2021.10-foss-2021b Seaborn/0.11.2-foss-2021b statsmodels/0.13.1-foss-2021b tqdm/4.62.3-GCCcore-11.2.0

Required By

This version of scanpy is a direct dependent of: scCODA/0.1.8-foss-2021b

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.

Version BEAR Apps Version
1.8.1-foss-2021a 2021a

Last modified on 2nd December 2022