aggregate_matrix | Aggregate matrix over groups |
annotation_plot | Plot brain structure annotation |
as_matrix | Convert dataframe to matrix |
assign_cells | Assign cells to structure |
brainspan_map | Project single cell gene expression data to BrainSpan |
de | Performs differential expression analysis on a sample x... |
deconvolute | Devonvolute bulk RNA-seq data based on reference data |
feature_plot | Feature plot |
get_aba_ref | Prepare ABA ISH reference for deconvolution |
get_markers | Get gene expression values from matrix |
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) |
log_message | Print diagnostic message |
mapping_plot | Plot correlation to entire brain or selected slices. |
mousebrain_map | Project single cell gene expression data to developing mouse... |
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 |
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 |
Print BrainSpanMap objects | |
reference_map | Compare a query scRNA-seq dataset with a reference |
run_epic | Run EPIC deconvolution |
safe_cor | Safe correlation function which returns a sparse matrix... |
slice_plot | Plot correlation to brain slices and structure annotation |
sparse_cor | Fast correlation for sparse matrices |
sparse_covcor | Fast correlation and covariance calcualtion for sparse... |
stage_name | Pick proper stage name |
structure_markers | Find differentially expressed features for all structures on... |
summarize_groups | Summarize data over groups |
summarize_structures | Summarize data over structures |
three_dim_plot | General 3D plotting function |
variable_genes | Finds variable features for all structures on a given... |
voxel_map | Project single cell gene expression data to spatial... |
zscale | Scale function that works for vectors and grouped dataframes |
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