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.