Index

A

append() (bioalpha.h5ad_map.SparseDatasetMap method) as_format() (bioalpha.h5ad_map.SparseDatasetMap method)

aucell() (in module bioalpha.singlecell.plotting) (in module bioalpha.singlecell.tools) aucell_heatmap() (in module bioalpha.singlecell.plotting)

B

batch_settings (in module bioalpha.h5ad_map) batch_size (in module bioalpha.h5ad_map) BatchReader (class in bioalpha.h5ad_map) bioalpha.singlecell.experimental module

bioalpha.singlecell.plotting module bioalpha.singlecell.preprocessing module bioalpha.singlecell.tools module

C

calculate_qc_metrics() (in module bioalpha.singlecell.preprocessing) chunk_X() (bioalpha.h5ad_map.H5ADMap method) chunked_X() (bioalpha.h5ad_map.H5ADMap method)

combine_keys() (in module bioalpha.singlecell.preprocessing) concatenate() (bioalpha.h5ad_map.H5ADMap method) copy() (bioalpha.h5ad_map.H5ADMap method)

D

data (bioalpha.h5ad_map.SparseDatasetMap property) diet_subset() (bioalpha.h5ad_map.H5ADMap method)

download_GEO_data() (in module bioalpha.singlecell) dtype (bioalpha.h5ad_map.SparseDatasetMap property)

F

file (bioalpha.h5ad_map.H5ADMap property) (bioalpha.h5ad_map.SparseDatasetMap property) filemode (bioalpha.h5ad_map.H5ADMap property) filename (bioalpha.h5ad_map.H5ADMap property) filter_cells() (in module bioalpha.singlecell.preprocessing)

filter_genes() (in module bioalpha.singlecell.preprocessing) find_marker() (in module bioalpha.singlecell.experimental.tools) flush() (bioalpha.h5ad_map.H5ADMap method) format_str (bioalpha.h5ad_map.SparseDatasetMap property) free_temp_processing() (bioalpha.h5ad_map.H5ADMap method) from_dataset() (bioalpha.h5ad_map.SparseDatasetMap static method)

G

get_gene_signatures_name_from_GSEA() (in module bioalpha.singlecell)

H

H5ADLoader (class in bioalpha.h5ad_map) H5ADMap (class in bioalpha.h5ad_map) h5py_group (bioalpha.h5ad_map.SparseDatasetMap property)

harmony_integrate() (in module bioalpha.singlecell.preprocessing) highest_expr_genes() (in module bioalpha.singlecell.plotting) highly_variable_genes() (in module bioalpha.singlecell.plotting) (in module bioalpha.singlecell.preprocessing)

I

indices (bioalpha.h5ad_map.SparseDatasetMap property) indptr (bioalpha.h5ad_map.SparseDatasetMap property)

init_writer() (bioalpha.h5ad_map.H5ADLoader method) is_view (bioalpha.h5ad_map.H5ADMap property) isbacked (bioalpha.h5ad_map.H5ADMap property)

K

kmeans() (in module bioalpha.singlecell.tools)

L

layers (bioalpha.h5ad_map.H5ADMap property) load() (bioalpha.h5ad_map.BatchReader method)

log1p() (in module bioalpha.singlecell.preprocessing) log_normalize() (in module bioalpha.singlecell.preprocessing) louvain() (in module bioalpha.singlecell.tools)

M

max_nnz_loading (in module bioalpha.h5ad_map) module bioalpha.singlecell.experimental bioalpha.singlecell.plotting bioalpha.singlecell.preprocessing bioalpha.singlecell.tools

N

n_loaded() (bioalpha.h5ad_map.BatchReader method) n_loads (bioalpha.h5ad_map.BatchReader property) n_obs (bioalpha.h5ad_map.H5ADMap property)

n_vars (bioalpha.h5ad_map.H5ADMap property) name (bioalpha.h5ad_map.SparseDatasetMap property) neighbors() (in module bioalpha.singlecell.preprocessing)

O

obs (bioalpha.h5ad_map.H5ADMap property) obs_keys() (bioalpha.h5ad_map.H5ADMap method) obs_names (bioalpha.h5ad_map.H5ADMap property) obs_names_make_unique() (bioalpha.h5ad_map.H5ADMap method)

obs_vector() (bioalpha.h5ad_map.H5ADMap method) obsm (bioalpha.h5ad_map.H5ADMap property) obsm_keys() (bioalpha.h5ad_map.H5ADMap method) obsp (bioalpha.h5ad_map.H5ADMap property)

P

pca() (in module bioalpha.singlecell.preprocessing)

R

rank_genes_groups() (in module bioalpha.singlecell.tools) rank_genes_groups_volcano() (in module bioalpha.singlecell.plotting) raw (bioalpha.h5ad_map.H5ADMap property) read_10x_h5() (in module bioalpha.singlecell) read_10x_mtx() (in module bioalpha.singlecell) read_gene_signatures() (in module bioalpha.singlecell) read_gene_signatures_gmt() (in module bioalpha.singlecell)

read_gene_signatures_GSEA() (in module bioalpha.singlecell) read_h5ad() (in module bioalpha.singlecell) read_mtx() (in module bioalpha.singlecell) reader (bioalpha.h5ad_map.H5ADLoader property) regress_out() (in module bioalpha.singlecell.preprocessing) rename_categories() (bioalpha.h5ad_map.H5ADMap method) reset() (bioalpha.h5ad_map.BatchReader method)

S

scale() (in module bioalpha.singlecell.preprocessing) set_backed() (bioalpha.h5ad_map.H5ADMap method) shape (bioalpha.h5ad_map.H5ADMap property) (bioalpha.h5ad_map.SparseDatasetMap property)

shuffle_ids (bioalpha.h5ad_map.BatchReader property) size (bioalpha.h5ad_map.BatchReader property) SparseDatasetMap (class in bioalpha.h5ad_map) strings_to_categoricals() (bioalpha.h5ad_map.H5ADMap method) subsample() (in module bioalpha.singlecell.preprocessing)

T

T (bioalpha.h5ad_map.H5ADMap property) thresholding() (in module bioalpha.singlecell.experimental.tools) to_backed() (bioalpha.h5ad_map.SparseDatasetMap method) to_csc() (bioalpha.h5ad_map.SparseDatasetMap method) to_csr() (bioalpha.h5ad_map.SparseDatasetMap method) to_dense() (bioalpha.h5ad_map.SparseDatasetMap method)

to_df() (bioalpha.h5ad_map.H5ADMap method) to_memory() (bioalpha.h5ad_map.H5ADMap method) (bioalpha.h5ad_map.SparseDatasetMap method) transfer() (bioalpha.h5ad_map.H5ADLoader method) transpose() (bioalpha.h5ad_map.H5ADMap method) tsne() (in module bioalpha.singlecell.plotting) (in module bioalpha.singlecell.tools)

U

umap() (in module bioalpha.singlecell.plotting) (in module bioalpha.singlecell.tools)

uns (bioalpha.h5ad_map.H5ADMap property) uns_keys() (bioalpha.h5ad_map.H5ADMap method)

V

value (bioalpha.h5ad_map.SparseDatasetMap property) var (bioalpha.h5ad_map.H5ADMap property) var_keys() (bioalpha.h5ad_map.H5ADMap method) var_names (bioalpha.h5ad_map.H5ADMap property)

var_names_make_unique() (bioalpha.h5ad_map.H5ADMap method) var_vector() (bioalpha.h5ad_map.H5ADMap method) varm (bioalpha.h5ad_map.H5ADMap property) varm_keys() (bioalpha.h5ad_map.H5ADMap method) varp (bioalpha.h5ad_map.H5ADMap property)

W

write() (bioalpha.h5ad_map.H5ADMap method) write_bioturing_format() (in module bioalpha.singlecell) write_csvs() (bioalpha.h5ad_map.H5ADMap method)

write_h5ad() (bioalpha.h5ad_map.H5ADMap method) write_loom() (bioalpha.h5ad_map.H5ADMap method) write_zarr() (bioalpha.h5ad_map.H5ADMap method) writer (bioalpha.h5ad_map.H5ADLoader property)

X

X (bioalpha.h5ad_map.H5ADMap property)