Get: get

The get module contains functions to extract information from the AnnData object.

Data Extraction

get.expr(adata, features[, groups, ...])	Extract the expression of features.
get.mean_expr(adata, group_by[, features, ...])	Calculate the average expression in an AnnData objects for features.
get.log2fc(adata, group_by, reference[, ...])	Calculate the log2foldchanges for a set of groups.
get.pcts_cells(adata, group_by[, features, ...])	Calculate the percentage of cells that express a feature.
get.dge_results(adata[, key, min_log2fc, ...])	Extract DEGs from AnnData object.

Object transformation

get.subset(adata[, obs_key, obs_groups, ...])	Subset AnnData object.
get.subset_df(df[, col, col_groups, comparison])	Subset Pandas DataFrame.
get.pseudobulk(adata, batch_key, cluster_key)	Generate pseudobulk AnnData of clusters.
get.layer_swap(adata, layer_key[, x_key, ...])	Swap adata.X with adata.layers.