scprep

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**Describe the bug** I am unable to run the test cases. They all complain with ``` E ModuleNotFoundError: No module named 'scprep' ``` **To Reproduce** Standalone code to reproduce the...

stkgo

A report by Erica in the Help Slack shows that the scprep google drive downloads are breaking in the workshop notebooks. Example: ``` # download the data from Google Drive...

atong01

scottgigante-immunai

**Describe the bug** `test_install_github` fails, preventing all PRs from passing **To Reproduce** ``` cd scprep pytest -v ``` **Expected behavior** Passes. **Actual behavior** Fails. ``` ====================================================================== ERROR: test_run.test_install_github_dependencies_None ---------------------------------------------------------------------- Traceback...

scottgigante-immunai

**Describe the bug** `test_slingshot` fails, preventing all PRs from passing **To Reproduce** ``` cd scprep pytest -v ``` **Expected behavior** Passes. **Actual behavior** Fails. ``` ====================================================================== ERROR: test_slingshot (test_run.TestSlingshot) ----------------------------------------------------------------------...

scottgigante-immunai

Hello! I really appreciate the wrapper you've built for the Slingshot function! It's the only way I found to use Slingshot from Python. However, I noticed something when trying to...

alex-claman

Density subsampling

1

**Describe the solution you'd like** scprep.select.subsample(density=True, knn=3). Use nmslib if available? **Describe alternatives you've considered** Use sklearn.NearestNeighbors

scottgigante

scottgigante

**Is your feature request related to a problem? Please describe.** Want to use louvain and leiden to produce a specific number of clusters **Describe the solution you'd like** ```python def...

dburkhardt

Set x/ylim in scprep.plot

1

Desired behavior: ```python scprep.plot.scatter2d(data_pca, ylim=(-1,1)) ```

dburkhardt