Reference API

abagen.allen - Primary workflows

Functions for mapping AHBA microarray dataset to atlases and and parcellations

abagen.get_expression_data(atlas[, ...])	Assigns microarray expression data to ROIs defined in atlas
abagen.get_samples_in_mask([mask])	Returns preprocessed microarray expression data for samples in mask
abagen.get_interpolated_map(genes, mask[, ...])	Generates dense (i.e., interpolated) expression maps for genes

abagen.datasets - Fetching AHBA datasets

Functions for fetching data relevant to the Allen Brain Atlas human microarray dataset

abagen.fetch_desikan_killiany([native, surface])	Fetches Desikan-Killiany atlas shipped with abagen
abagen.fetch_donor_info()	Returns dataframe with donor demographic information
abagen.fetch_freesurfer([data_dir, donors, ...])	Downloads FreeSurfer reconstructions of the Allen Human Brain Atlas MRIs
abagen.fetch_gene_group(group)	Return list of gene acronyms belonging to provided group
abagen.fetch_microarray([data_dir, donors, ...])	Downloads the Allen Human Brain Atlas microarray expression dataset
abagen.fetch_raw_mri([data_dir, donors, ...])	Downloads the "raw" Allen Human Brain Atlas T1w/T2w MRI images
abagen.fetch_rnaseq([data_dir, donors, ...])	Downloads RNA-sequencing data from the Allen Human Brain Atlas
abagen.datasets.fetch_fsaverage5([load])	Fetches and optionally loads fsaverage5 surface
abagen.datasets.fetch_fsnative(donors[, ...])	Fetches and optionally loads fsnative surface of donor

abagen.images - Image processing functions

abagen.leftify_atlas(atlas)	Zeroes out all ROIs in the right hemisphere of volumetric atlas
abagen.check_atlas(atlas[, atlas_info, ...])	Checks that atlas is a valid atlas
abagen.annot_to_gifti(atlas)	Converts FreeSurfer-style annotation file atlas to in-memory GIFTI image
abagen.relabel_gifti(atlas[, background, offset])	Updates GIFTI images so label IDs are consecutive across hemispheres

abagen.correct - Post-processing corrections

Functions for processing and correcting gene expression data

abagen.remove_distance(coexpression, atlas)	Corrects for distance-dependent correlation effects in coexpression
abagen.keep_stable_genes(expression[, ...])	Removes genes in expression with differential stability < threshold
abagen.normalize_expression(expression[, ...])	Performs normalization on expression data

abagen.matching - Functions for matching samples

Structures and functions used for matching samples to atlas

abagen.AtlasTree(atlas[, coords, triangles, ...])

Representation of a parcellation as a cKDtree for NN lookups

abagen.matching.get_centroids(data, coordinates)	Finds centroids of data in coordinates space
abagen.matching.closest_centroid(coords, ...)	Returns index of centroids closest to coords (Euclidean distance)

abagen.reporting - Functions for generating reports

Functions for generating workflow methods reports

Note: all text contained within this module is released under a CC-0 license.

abagen.Report(atlas[, atlas_info, ...])

Generates report of methods for abagen.get_expression_data()

abagen.io - Loading AHBA data files

Functions for loading the various files associated with the AHBA microarray and RNAseq datasets.

This also contains functionality for optionally converting the downloaded CSV files to parquet format, which provides much faster I/O access / quicker load times.

abagen.io.read_annotation(fname[, copy])	Loads SampleAnnot.csv file found at fname
abagen.io.read_microarray(fname[, copy, parquet])	Loads MicroarrayExpression.csv file found at fname
abagen.io.read_ontology(fname[, copy])	Loads Ontology.csv file found at fname
abagen.io.read_pacall(fname[, copy, parquet])	Loads PACall.csv file found at fname
abagen.io.read_probes(fname[, copy])	Loads Probes.csv file found at fname
abagen.io.read_genes(fname[, copy])	Loads Genes.csv file found at fname
abagen.io.read_tpm(fname[, copy])	Loads RNAseqTPM.csv file found at fname
abagen.io.read_counts(fname[, copy])	Loads RNAseqCounts.csv file found at fname

abagen.mouse - Working with the Allen Mouse Brain Atlas

abagen.mouse.available_gene_info()	Lists available attributes for abagen.mouse.get_gene_info()
abagen.mouse.available_structure_info()	Lists available attributes for abagen.mouse.get_structure_info()
abagen.mouse.available_unionization_info()	Lists attributes for abagen.mouse.get_unionization_from_gene()
abagen.mouse.get_gene_info([id, acronym, ...])	Queries Allen API for information about given gene
abagen.mouse.get_structure_info([id, ...])	Queries Allen API for information about given gene
abagen.mouse.get_structure_coordinates([id, ...])	Finds xyz coordinates of provided structure(s) in reference_space
abagen.mouse.get_unionization_from_gene([...])	Gets unionization data for provided gene(s)
abagen.mouse.fetch_allenref_genes([...])	Loads all genes from Allen Reference database
abagen.mouse.fetch_allenref_structures([...])	Loads all anatomical structures in the Allen Reference Atlas
abagen.mouse.fetch_rubinov2015_structures([...])	Loads subset of anatomical structures in Allen Reference Atlas from [MI1]