Preprocessing: pp

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

sc/snRNA Processing

pp.run_cellbender(cellranger_path, output_path)	Run cellbender to remove ambient RNA.
pp.importer_py(paths, ids[, metadata, ...])	Quality control analysis for sc/snRNA.
pp.quality_control(adata[, batch_key, ...])	Basic quality control for sc/snRNA-seq.
pp.log_normalize(adata[, target_sum])	Apply LogNormalization.
pp.sctransform_normalize(adata[, batch_key, ...])	Normalization based on SCTransform.
pp.find_doublets(adata[, batch_key, ...])	Detect doublets in scRNAseq and iST.