tacco.tools

Tools for annotation transfer and related tasks

Functions

affinity	Calculates an affinity from a distance matrix.
annotate	Annotates an AnnData using reference data.
annotate_NMFreg	Annotates an AnnData using reference data by NMFreg [Rodriques19].
annotate_OT	Annotates an AnnData using reference data by semi-balanced optimal transport.
annotate_RCTD	Annotates an AnnData using reference data by RCTD [Cable21].
annotate_SingleR	Annotates an AnnData using reference data by SingleR [Aran19].
annotate_nnls	Annotates an AnnData using reference data by NNLS (non-negative least squares).
annotate_novosparc	Annotates an AnnData using reference data by NovoSpaRc [Nitzan19].
annotate_projection	Annotates an AnnData using reference data by projection.
annotate_single_molecules	Annotates single molecules in space using reference data.
annotate_svm	Annotates an AnnData using reference data by an SVM [Abdelaal19].
annotate_tangram	Annotates an AnnData using reference data by Tangram [Biancalani20].
annotate_wot	Annotates an AnnData using reference data by Waddington-OT [Schiebinger19].
annotation_coordinate	Calculates a distance-like quantity from an annotation in space.
co_occurrence	Calculates a spatial co-occurence score given by the conditional probability to find an annotation a at some distance d from an observation with annotation b, normalized by the probability to find an annotation a at distance d from an observation disregarding the value of its annotation: p(a|bd)/p(a|d).
co_occurrence_matrix	Calculates a spatial co-occurence score given by the conditional probability to find an annotation a at some distance d from an observation with annotation b, normalized by the probability to find an annotation a at distance d from an observation disregarding the value of its annotation: p(a|bd)/p(a|d).
distance_matrix	Calculates a sparse or dense distance matrix.
distribute_molecules	Distributes the counts of observations randomly in space.
enrichments	Find enrichments in groups.
fill_regions	Fills the region annotation of not annotated observation (i.e. na values) with the annotation of the spatially closest annotated observation.
find_regions	Find regions in position space defined by proximity in position space and in expression (or annotation) space.
get_compositions	Get the compositions of groups.
get_contributions	Get the contributions of groups.
merge_observations	Merges equivalent observations of an AnnData by summing over the expression.
mix_in_silico	Given single cell data, create an in-silico mixed dataset.
run_goa_analysis	Run a GO analysis.
run_orthology_converter	Run orthology conversion between species using MGI homology information information (Mouse Genome Informatics Web Site, http://www.informatics.jax.org/homology.shtml).
segment	Segment single molecules in space to get a cell-like annotation.
setup_goa_analysis	Setup a GO analysis.
setup_orthology_converter	Setup for converting gene names between species using MGI homology information (Mouse Genome Informatics Web Site, http://www.informatics.jax.org/homology.shtml).
spectral_clustering	Performs spectral clustering on an affinity matrix.
split_observations	Splits expression data with a "soft" weights annotation in .obsm into multiple "virtual" observations per input observation e.g. splits expression data for cell type mixtures with annotated cell type fractions into expression of single type observations with categorical annotation.