Function reference • VoxHunt

Data loading Functions for loading reference data
`load_aba_data()`	Define the path to voxel data and load lazily if required
`load_mousebrain_data()`	Load the mousebrain data (LaManno & Siletti et al. 2020)
Marker discovery Functions to find brain structure markers
`structure_markers()`	Find differentially expressed features for all structures on a given annotation level
`variable_genes()`	Finds variable features for all structures on a given annotation level
Reference mapping Functions to perform comparisons with different references
`voxel_map()`	Project single cell gene expression data to spatial expression patterns in the mouse brain
`brainspan_map()`	Project single cell gene expression data to BrainSpan
`mousebrain_map()`	Project single cell gene expression data to developing mouse brain data (LaManno & Siletti et al. 2020)
`reference_map()`	Compare a query scRNA-seq dataset with a reference
Deconvolution Functions to perform reference-based deconvolution of RNA-seq data
`deconvolute()`	Devonvolute bulk RNA-seq data based on reference data
Visualization Plotting functions to visualize marker expression and mapping results
`plot_annotation()`	Plot brain structure annotation
`plot_expression()`	Plot gene expression across the mouse brain
`plot_expression_3d()`	Plot gene expression across the mouse brain in 3D
`plot_map()`	Plot similarity map of single cells
`plot_map_3d()`	Plot similarity map of single cells to voxels in 3D
`plot_structure_similarity()`	Plot similarity to brain structures
`no_legend()`	Remove legend from plot
`no_text()`	Remove text from plot
`no_x_text()`	Remove x-axis text from plot
`no_y_text()`	Remove y-axis text from plot
Utilities Utility functions for plotting and summarizing results
`summarize_groups()`	Summarize data over groups
`summarize_structures()`	Summarize data over structures
`assign_cells()` `assign_to_structure()`	Assign cells to structure
`as_matrix()`	Convert dataframe to matrix
`no_legend()`	Remove legend from plot
`no_text()`	Remove text from plot
`no_x_text()`	Remove x-axis text from plot
`no_y_text()`	Remove y-axis text from plot

Reference

Data loading

Marker discovery

Reference mapping

Deconvolution

Visualization

Utilities