Preprocessing: pp

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Preprocessing: pp#

The preprocessing module dotools_py.pp compiles all the basic quality control steps for analyzing sc/snRNA-seq and Visium with different implementations building on packages from the scverse ecosystem

Processing#

pp.run_cellbender(cellranger_path, output_path)

Run cellbender to remove ambient RNA.

pp.importer_py(paths, ids[, metadata, ...])

Quality control analysis for scRNA / Spatial Transcriptomics.

pp.quality_control(adata, batch_key[, ...])

Basic quality control for snRNA-seq / Spatial Transcriptomics.

pp.log_normalize(adata[, target_sum, log_data])

Apply LogNormalization.

pp.pearson_residuals_normalize(adata[, ...])

Apply analytic Pearson residual normalization.

pp.find_doublets(adata[, batch_key, ...])

Detect doublets in scRNAseq and iST.
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