Index

A

arcsinh() (in module scprep.transform)

AutomaticDimensionSVD (class in scprep.reduce)

B

batch_mean_center() (in module scprep.normalize)

C

check_consistent_columns() (in module scprep.utils)

combine_batches() (in module scprep.utils) components_() (scprep.reduce.SparseInputPCA property)

D

differential_expression() (in module scprep.stats) differential_expression_by_cluster() (in module scprep.stats) download_and_extract_zip() (in module scprep.io.download)

download_google_drive() (in module scprep.io.download) download_url() (in module scprep.io.download) DyngenSimulate() (in module scprep.run)

E

EMD() (in module scprep.stats)

explained_variance_() (scprep.reduce.SparseInputPCA property) explained_variance_ratio_() (scprep.reduce.SparseInputPCA property)

F

filter_duplicates() (in module scprep.filter) filter_empty_cells() (in module scprep.filter) filter_empty_genes() (in module scprep.filter) filter_gene_set_expression() (in module scprep.filter) filter_library_size() (in module scprep.filter) filter_rare_genes() (in module scprep.filter)

filter_values() (in module scprep.filter) fit() (scprep.reduce.AutomaticDimensionSVD method) (scprep.reduce.InvertibleRandomProjection method) (scprep.reduce.SparseInputPCA method) fit_transform() (scprep.reduce.AutomaticDimensionSVD method) (scprep.reduce.InvertibleRandomProjection method) (scprep.reduce.SparseInputPCA method)

G

gene_capture_count() (in module scprep.measure) gene_set_expression() (in module scprep.measure) gene_variability() (in module scprep.measure) get_cell_set() (in module scprep.select) get_gene_set() (in module scprep.select)

get_node() (in module scprep.io.hdf5) get_params() (scprep.reduce.AutomaticDimensionSVD method) (scprep.reduce.InvertibleRandomProjection method) (scprep.reduce.SparseInputPCA method) get_values() (in module scprep.io.hdf5)

H

highly_variable_genes() (in module scprep.select)

histogram() (in module scprep.plot)

I

install() (in module scprep.run.slingshot) (in module scprep.run.splatter) install_bioconductor() (in module scprep.run)

install_github() (in module scprep.run) inverse_transform() (scprep.reduce.AutomaticDimensionSVD method) (scprep.reduce.SparseInputPCA method) InvertibleRandomProjection (class in scprep.reduce)

J

jitter() (in module scprep.plot)

K

knnDREMI() (in module scprep.stats)

L

library_size() (in module scprep.measure) library_size_normalize() (in module scprep.normalize) list_nodes() (in module scprep.io.hdf5) load_10X() (in module scprep.io) load_10X_HDF5() (in module scprep.io)

load_10X_zip() (in module scprep.io) load_csv() (in module scprep.io) load_fcs() (in module scprep.io) load_mtx() (in module scprep.io) load_tsv() (in module scprep.io) log() (in module scprep.transform)

M

marker_plot() (in module scprep.plot) matrix_any() (in module scprep.utils) matrix_min() (in module scprep.utils) matrix_non_negative() (in module scprep.utils) matrix_std() (in module scprep.utils)

matrix_sum() (in module scprep.utils) matrix_transform() (in module scprep.utils) matrix_transpose() (in module scprep.utils) matrix_vector_elementwise_multiply() (in module scprep.utils) mean_difference() (in module scprep.stats) mutual_information() (in module scprep.stats)

O

open_file() (in module scprep.io.hdf5)

P

pairwise_correlation() (in module scprep.stats) pca() (in module scprep.reduce) plot_gene_set_expression() (in module scprep.plot)

plot_gene_variability() (in module scprep.plot) plot_knnDREMI() (in module scprep.stats) plot_library_size() (in module scprep.plot) pseudoinverse() (scprep.reduce.InvertibleRandomProjection property)

R

rank_sum_statistic() (in module scprep.stats)

RFunction (class in scprep.run) rotate_scatter3d() (in module scprep.plot)

S

save_mtx() (in module scprep.io) scatter() (in module scprep.plot) scatter2d() (in module scprep.plot) scatter3d() (in module scprep.plot) scprep.filter (module) scprep.io (module) scprep.io.download (module) scprep.io.hdf5 (module) scprep.measure (module) scprep.normalize (module) scprep.plot (module) scprep.reduce (module) scprep.run (module) scprep.run.slingshot (module) scprep.run.splatter (module) scprep.select (module) scprep.stats (module)

scprep.transform (module) scprep.utils (module) scree_plot() (in module scprep.plot) select_cols() (in module scprep.select) select_rows() (in module scprep.select) set_params() (scprep.reduce.AutomaticDimensionSVD method) (scprep.reduce.InvertibleRandomProjection method) (scprep.reduce.SparseInputPCA method) singular_values_() (scprep.reduce.SparseInputPCA property) Slingshot() (in module scprep.run) (in module scprep.run.slingshot) sort_clusters_by_values() (in module scprep.utils) sparse_series_min() (in module scprep.utils) SparseInputPCA (class in scprep.reduce) SplatSimulate() (in module scprep.run) (in module scprep.run.splatter) sqrt() (in module scprep.transform) subsample() (in module scprep.select)

T

t_statistic() (in module scprep.stats) to_array_or_spmatrix() (in module scprep.utils) toarray() (in module scprep.utils)

transform() (scprep.reduce.AutomaticDimensionSVD method) (scprep.reduce.InvertibleRandomProjection method) (scprep.reduce.SparseInputPCA method)

U

unzip() (in module scprep.io.download)