Replace deprecated `sc.pp.normalize_per_cell` with `sc.pp.normalize_total`

dylkot / cNMF

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

MIT License

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Replace deprecated `sc.pp.normalize_per_cell` with `sc.pp.normalize_total` #67

Closed scottgigante-immunai closed 1 month ago

scottgigante-immunai commented 1 year ago

normalize_per_cell raises numpy.core._exceptions.UFuncTypeError (see https://github.com/scverse/scanpy/issues/2500) and is deprecated.

dylkot commented 1 month ago

Hi @scottgigante-immunai I fixed this on the development branch using sc.pp.normalize_total() as was suggested and will update it to the main and pypi in the next week. Thanks!