dynamo.pp.CnmfPreprocessor

class dynamo.pp.CnmfPreprocessor(**kwargs)[source]

A specialized preprocessor based on cNMF. Args used are the same as normal Preprocessor.

__init__(**kwargs)[source]

A specialized preprocessor based on cNMF. Args used are the same as normal Preprocessor.

Methods

__init__(**kwargs)

A specialized preprocessor based on cNMF.

add_experiment_info(adata[, tkey, ...])

Infer the experiment type and experiment layers stored in the AnnData object and record the info in unstructured metadata (.uns).

cleanup_cnmf()

Remove the tmp folder to store data used for cNMF.

config_monocle_pearson_residuals_recipe(adata)

Automatically configure the preprocessor for using the Monocle-Pearson-residuals style recipe.

config_monocle_recipe(adata[, n_top_genes])

Automatically configure the preprocessor for monocle recipe.

config_pearson_residuals_recipe(adata)

Automatically configure the preprocessor for using the Pearson residuals style recipe.

config_sctransform_recipe(adata)

Automatically configure the preprocessor for using the sctransform style recipe.

config_seurat_recipe(adata)

Automatically configure the preprocessor for using the seurat style recipe.

k_selection_plot()

Plot the K selection curve of cNMF and save to the output folder.

preprocess_adata(adata)

Preprocess the AnnData object with cNMF.

preprocess_adata_monocle(adata[, tkey, ...])

Preprocess the AnnData object based on Monocle style preprocessing recipe.

preprocess_adata_monocle_pearson_residuals(adata)

A combined pipeline of monocle and pearson_residuals.

preprocess_adata_pearson_residuals(adata[, ...])

A pipeline proposed in Pearson residuals (Lause, Berens & Kobak, 2021).

preprocess_adata_sctransform(adata[, tkey, ...])

Python implementation of https://github.com/satijalab/sctransform.

preprocess_adata_seurat(adata[, tkey, ...])

The preprocess pipeline in Seurat based on dispersion, implemented by dynamo authors.

preprocess_adata_seurat_wo_pca(adata[, ...])

Preprocess the anndata object according to standard preprocessing in Seurat recipe without PCA.

standardize_adata(adata, tkey, experiment_type)

Process the AnnData object to make it meet the standards of dynamo.