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abagen

Reference API

List of modules

abagen.allen - Primary workflows

abagen.allen

abagen

abagen.get_expression_data abagen.get_samples_in_mask abagen.get_interpolated_map

abagen.datasets - Fetching AHBA datasets

abagen.datasets

abagen

abagen.fetch_desikan_killiany abagen.fetch_donor_info abagen.fetch_freesurfer abagen.fetch_gene_group abagen.fetch_microarray abagen.fetch_raw_mri abagen.fetch_rnaseq abagen.datasets.fetch_fsaverage5 abagen.datasets.fetch_fsnative

abagen.images - Image processing functions

abagen.images

abagen

abagen.leftify_atlas abagen.check_atlas abagen.annot_to_gifti abagen.relabel_gifti

abagen.correct - Post-processing corrections

abagen.correct

abagen

abagen.remove_distance abagen.keep_stable_genes abagen.normalize_expression

abagen.matching - Functions for matching samples

abagen.matching

abagen

abagen.AtlasTree

abagen

abagen.matching.get_centroids abagen.matching.closest_centroid

abagen.reporting - Functions for generating reports

abagen.reporting

abagen

abagen.Report

abagen.io - Loading AHBA data files

abagen.io

abagen.io

abagen.io.read_annotation abagen.io.read_microarray abagen.io.read_ontology abagen.io.read_pacall abagen.io.read_probes abagen.io.read_genes abagen.io.read_tpm abagen.io.read_counts

abagen.mouse - Working with the Allen Mouse Brain Atlas

abagen.mouse

abagen.mouse

abagen.mouse.available_gene_info abagen.mouse.available_structure_info abagen.mouse.available_unionization_info

abagen.mouse.get_gene_info abagen.mouse.get_structure_info abagen.mouse.get_structure_coordinates abagen.mouse.get_unionization_from_gene

abagen.mouse.fetch_allenref_genes abagen.mouse.fetch_allenref_structures abagen.mouse.fetch_rubinov2015_structures