BEAR Applications

cell2location 0.05-alpha-fosscuda-2020b

There is a newer version of cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

Accessing cell2location 0.05-alpha-fosscuda-2020b

To load the module for cell2location 0.05-alpha-fosscuda-2020b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load cell2location/0.05-alpha-fosscuda-2020b

There is a CPU version of this module: cell2location 0.05-alpha-foss-2020b

BEAR Apps Version

2020h

Extensions

• anndata 0.7.5
• annoy 1.17.0
• bbknn 1.3.12
• cell2location-0.05-alpha
• descartes 1.1.0
• get_version 2.1
• ipykernel 5.3.4
• legacy-api-wrap-1.2
• loompy 3.0.6
• louvain 0.7.0
• mizani 0.7.1
• natsort 7.1.0
• nose 1.3.7
• numpy-groupies-0.9.13
• opt-einsum-3.3.0
• palettable 3.3.0
• plotnine 0.7.0
• pytoml 0.1.21
• scanpy 1.6.0
• sinfo 0.3.1
• stdlib-list-0.8.0

More Information

For more information visit the cell2location website.

Dependencies

This version of cell2location has a direct dependency on: CMake/3.18.4-GCCcore-10.2.0 dill/0.3.3-GCCcore-10.2.0 fosscuda/2020b hyperopt/0.2.5-fosscuda-2020b IPython/7.18.1-GCCcore-10.2.0 Java/11 leidenalg/0.8.3-fosscuda-2020b libgpuarray/0.7.6-fosscuda-2020b libtool/2.4.6-GCCcore-10.2.0 matplotlib/3.3.3-fosscuda-2020b numba/0.52.0-fosscuda-2020b PyMC3/3.11.1-fosscuda-2020b pyro-api/0.1.2-fosscuda-2020b pyro-ppl/1.5.2-fosscuda-2020b PyTables/3.6.1-fosscuda-2020b Python/3.8.6-GCCcore-10.2.0 PyTorch/1.7.1-fosscuda-2020b request/2.88.1-fosscuda-2020b-nodejs-12.19.0 SciPy-bundle/2020.11-fosscuda-2020b Seaborn/0.11.1-fosscuda-2020b statsmodels/0.12.1-fosscuda-2020b Theano/1.1.2-fosscuda-2020b-PyMC umap-learn/0.4.6-fosscuda-2020b

Other Versions

These versions of cell2location 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 28th July 2021