Index

_

__bool__() (topact.constantlookuplist.ConstantLookupList method) __contains__() (topact.constantlookuplist.ConstantLookupList method) __delitem__() (topact.constantlookuplist.ConstantLookupList method) __getitem__() (topact.constantlookuplist.ConstantLookupList method) __iter__() (topact.constantlookuplist.ConstantLookupList method) __len__() (topact.constantlookuplist.ConstantLookupList method) __repr__() (topact.constantlookuplist.ConstantLookupList method) __reversed__() (topact.constantlookuplist.ConstantLookupList method)

__setitem__() (topact.constantlookuplist.ConstantLookupList method) __str__() (topact.constantlookuplist.ConstantLookupList method) __version__ (in module topact) _apply_or_not() (in module topact.countdata) _flatten_coords() (topact.spatial.ExpressionGrid method) _flatten_coords_vec() (topact.spatial.ExpressionGrid method) _generate_lookup() (topact.constantlookuplist.ConstantLookupList method) _get_pad() (in module topact.densetools) _get_slice() (in module topact.densetools)

A

add_metadata() (topact.countdata.CountData method)

annotate() (topact.spatial.CountGrid method) avg_expression() (topact.countdata.CountMatrix method)

C

cartesian_product() (in module topact.spatial) classes (topact.classifier.Classifier attribute) Classifier (class in topact.classifier) classify() (topact.classifier.Classifier method) (topact.classifier.SVCClassifier method) classify_parallel() (topact.spatial.CountGrid method) cols() (topact.spatial.ExpressionGrid method)

combine_coords() (in module topact.spatial) ConstantLookupList (class in topact.constantlookuplist) count() (topact.constantlookuplist.ConstantLookupList method) count_matrix() (topact.spatial.CountGrid method) CountData (class in topact.countdata) CountGrid (class in topact.spatial) CountMatrix (class in topact.countdata) CountTable (class in topact.countdata)

D

density() (in module topact.densetools) density_hull() (in module topact.densetools)

density_mask() (topact.spatial.CountGrid method) differentially_expressed() (in module topact.filtering)

E

expressed_genes() (topact.countdata.CountMatrix method) expression() (topact.countdata.CountMatrix method) (topact.spatial.ExpressionGrid method) expression_modulo_metadata() (in module topact.filtering)

expression_vec() (topact.spatial.ExpressionGrid method) ExpressionGrid (class in topact.spatial) extract_classifications() (in module topact.spatial) extract_image() (in module topact.spatial)

F

filter_cols() (in module topact.sparsetools) filter_genes() (in module topact.filtering) (topact.countdata.CountData method) (topact.countdata.CountMatrix method) (topact.countdata.CountTable method)

first_coord() (in module topact.spatial) first_nonzero_1d() (in module topact.densetools) first_nonzero_2d() (in module topact.densetools) from_coord_table() (topact.spatial.CountGrid class method)

G

generate_expression_grid() (topact.spatial.CountGrid method) genes (topact.countdata.CountData attribute) (topact.countdata.CountTable attribute)

grid (topact.spatial.CountGrid attribute) group_by_metadata() (topact.countdata.CountData method)

H

height (topact.spatial.ExpressionGrid attribute)

highly_expressed_columns() (in module topact.filtering)

I

index() (topact.constantlookuplist.ConstantLookupList method)

insert() (topact.constantlookuplist.ConstantLookupList method) iterate_sparse() (in module topact.sparsetools)

L

last_nonzero_2d() (in module topact.densetools)

log_fold_change() (in module topact.filtering)

M

match_by_metadata() (topact.countdata.CountData method) matching() (in module topact.countdata) matrix (topact.countdata.CountMatrix attribute) metadata (topact.countdata.CountData attribute) (topact.countdata.CountTable attribute) module topact topact.classifier topact.constantlookuplist topact.countdata topact.densetools topact.filtering topact.sparsetools topact.spatial

N

normalize_rows() (in module topact.classifier) num_genes (topact.countdata.CountData attribute) (topact.countdata.CountTable attribute)

num_samples (topact.countdata.CountData attribute) (topact.countdata.CountTable attribute)

P

pool() (in module topact.densetools)

pseudobulk() (topact.spatial.CountGrid method)

R

rescale() (in module topact.sparsetools) rescale_columns() (in module topact.sparsetools) rescale_genes() (topact.countdata.CountMatrix method)

rescale_rows() (in module topact.sparsetools) reverse() (topact.constantlookuplist.ConstantLookupList method) rows() (topact.spatial.ExpressionGrid method) run() (topact.spatial.Worker method)

S

samples (topact.countdata.CountData attribute) (topact.countdata.CountTable attribute) second_coord() (in module topact.spatial) split_coords() (in module topact.spatial)

square_nbhd() (in module topact.spatial) (topact.spatial.ExpressionGrid method) square_nbhd_vec() (in module topact.spatial) (topact.spatial.ExpressionGrid method) SVCClassifier (class in topact.classifier)

T

to_count_table() (topact.countdata.CountMatrix method) toCountMatrix() (topact.countdata.CountTable method) topact module topact.classifier module topact.constantlookuplist module topact.countdata module topact.densetools module

topact.filtering module topact.sparsetools module topact.spatial module train() (topact.classifier.Classifier method) (topact.classifier.SVCClassifier method) train_from_countmatrix() (in module topact.classifier) trained (topact.classifier.Classifier attribute) translate() (in module topact.densetools)

W

width (topact.spatial.ExpressionGrid attribute)

Worker (class in topact.spatial)

X

x_max (topact.spatial.ExpressionGrid attribute)

x_min (topact.spatial.ExpressionGrid attribute)

Y

y_max (topact.spatial.ExpressionGrid attribute)

y_min (topact.spatial.ExpressionGrid attribute)