There is a newer version of scanpyScanpy 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
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.
- anndata 0.7.6
- natsort 7.1.1
- pynndescent 0.5.4
- scanpy 1.8.1
- sinfo 0.3.4
- xlrd 1.2.0
For more information visit the scanpy website.
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
This version of scanpy is a direct dependent of: scVelo/0.2.4-foss-2021a
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.
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Last modified on 20th May 2022