Man pages for quadbiolab/VoxHunt
Projecting single-cell transcriptomes to spatial brain maps
| 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 |
