AnnData

adata_dict utility functions for anndata. Some of these ease manipulation of and information retrieval from AnnData.

Get column names from adata.obs with string matching

get_adata_columns(adata[, starts_with, ...])

A simple string matching and filtering function to get column names from adata.obs.

Remove genes

remove_genes(adata, genes_to_remove[, adt_key])

Remove specified genes from an AnnData object in-place.

Add metadata

add_col_to_adata_obs(adata, indices, values, ...)	Adds a column to adata.obs for given indices.
add_col_to_adata_var(adata, indices, values, ...)	Adds a column to adata.var for given indices.
add_col_to_pd_df(pd_df, indices, values, ...)	Adds a column to pd_df for given indices.

Convert column dtypes

convert_obs_col_to_category(adata, cols)	Convert column(s) in adata.obs to category dtype.
convert_obs_col_to_string(adata, cols)	Convert column(s) in adata.obs to str dtype.
convert_obs_index_to_str(adata)	Converts the index of adata.obs to str.

Filter a list of genes based on their presence in adata.var.index

filter_gene_list(adata, gene_list)

Filter a list of genes based on their presence in adata.var.index.