| apply_combat | Apply ComBat batch correction to pseudobulk matrices.... |
| calculate_fiber_fstats | Calculate F-Statistics for the association between donor... |
| check_rec_pres | Helper function to check whether receptor is present in... |
| clean_data | Clean data to remove genes only expressed in a few cells and... |
| colMeanVars | Calculates column mean and variance. Adapted from pagoda2.... |
| compare_decompositions | Plot a pairwise comparison of factors from two separate... |
| compute_associations | Compute associations between donor proportions and factor... |
| compute_donor_props | Get donor proportions of each cell type or subtype |
| compute_LR_interact | Compute and plot the LR interactions for one factor |
| convert_gn | Convert gene identifiers to gene symbols |
| count_word | count_word. From older version of simplifyEnrichment package. |
| determine_ranks_tucker | Run rank determination by svd on the tensor unfolded along... |
| form_tensor | Form the pseudobulk tensor as preparation for running the... |
| get_all_lds_factor_plots | Generate loadings heatmaps for all factors |
| get_callouts_annot | Get gene callout annotations for a loadings heatmap |
| get_ctype_exp_var | Get explained variance of the reconstructed data using one... |
| get_ctype_prop_associations | Compute and plot associations between donor factor scores and... |
| get_ctype_subc_prop_associations | Compute and plot associations between donor factor scores and... |
| get_ctype_vargenes | Partition main gene by cell matrix into per cell type... |
| get_donor_meta | Get metadata matrix of dimensions donors by variables (not... |
| get_factor_exp_var | Get the explained variance of the reconstructed data using... |
| get_fstats_pvals | Calculate adjusted p-values for gene_celltype fiber-donor... |
| get_gene_modules | Compute WGCNA gene modules for each cell type |
| get_gene_set_vectors | Get logical vectors indicating which genes are in which... |
| get_indv_subtype_associations | Compute subtype proportion-factor association p-values for... |
| get_intersecting_pathways | Extract the intersection of gene sets which are enriched in... |
| get_leading_edge_genes | Get the leading edge genes from GSEA results |
| get_lm_pvals | Compute gene-factor associations using univariate linear... |
| get_max_correlations | Computes the max correlation between each factor of the... |
| get_meta_associations | Get metadata associations with factor donor scores |
| get_min_sig_genes | Evaluate the minimum number for significant genes in any... |
| get_module_enr | Identify gene sets that are enriched within specified gene... |
| get_normalized_variance | Get normalized variance for each gene, taking into account... |
| get_num_batch_ranks | Plot factor-batch associations for increasing number of donor... |
| get_one_factor | Get the donor scores and loadings matrix for a single-factor |
| get_one_factor_gene_pvals | Get significant genes for a factor |
| get_pseudobulk | Collapse data from cell-level to donor-level via summing... |
| get_real_fstats | Get F-Statistics for the real (non-shuffled) gene_ctype... |
| get_reconstruct_errors_svd | Calculate reconstruction errors using svd approach |
| get_significance_vectors | Get vectors indicating which genes are significant in which... |
| get_subclust_de_hmaps | Get list of cell subtype differential expression heatmaps |
| get_subclust_enr_dotplot | Get scatter plot for association of a cell subtype proportion... |
| get_subclust_enr_fig | Get a figure showing cell subtype proportion associations... |
| get_subclust_enr_hmap | Get heatmap of subtype proportion associations for each... |
| get_subclusters | Perform leiden subclustering to get cell subtypes |
| get_subclust_umap | Get a figure to display subclusterings at multiple... |
| get_subtype_prop_associations | Compute and plot associations between factor scores and cell... |
| get_sums | Calculates factor-stratified sums for each column. Adapted... |
| ht_clusters | Visualize the similarity matrix and the clustering. Adapted... |
| identify_sex_metadata | Extract metadata for sex information if not provided already |
| initialize_params | Initialize parameters to be used throughout scITD in various... |
| instantiate_scMinimal | Create an scMinimal object. Generally, this should be done... |
| is_GO_id | Check if a character is a go ID |
| make_new_container | Create a container to store all data and results for the... |
| merge_small_clusts | Merge small subclusters into larger ones |
| nmf_unfolded | Computes non-negative matrix factorization on the tensor... |
| normalize_counts | Helper function to normalize and log-transform count data |
| normalize_pseudobulk | Normalize the pseudobulked counts matrices. Generally, this... |
| norm_var_helper | Calculates the normalized variance for each gene. This is... |
| parse_data_by_ctypes | Parse main counts matrix into per-celltype-matrices.... |
| pca_unfolded | Computes singular-value decomposition on the tensor unfolded... |
| plotDEheatmap_conos | Plot a heatmap of differential genes. Code is adapted from... |
| plot_donor_matrix | Plot matrix of donor scores extracted from Tucker... |
| plot_donor_props | Plot donor celltype/subtype proportions against each factor |
| plot_donor_sig_genes | Generate a gene by donor heatmap showing scaled expression of... |
| plot_dscore_enr | Compute enrichment of donor metadata categorical variables at... |
| plot_gsea_hmap | Plot enriched gene sets from all cell types in a heatmap |
| plot_gsea_hmap_w_similarity | Plot already computed enriched gene sets to show semantic... |
| plot_gsea_sub | Look at enriched gene sets from a cluster of semantically... |
| plot_loadings_annot | Plot the gene by celltype loadings for a factor |
| plot_mod_and_lig | Plot trio of associations between ligand expression, module... |
| plot_multi_module_enr | Generate gene set x ct_module heatmap showing co-expression... |
| plot_rec_errors_bar_svd | Plot reconstruction errors as bar plot for svd method |
| plot_rec_errors_line_svd | Plot reconstruction errors as line plot for svd method |
| plot_scores_by_meta | Plot dotplots for each factor to compare donor scores between... |
| plot_select_sets | Plot enrichment results for hand picked gene sets |
| plot_stability_results | Generate a plot for either the donor scores or loadings... |
| plot_subclust_associations | Plot association significances for varying clustering... |
| prep_LR_interact | Prepare data for LR analysis and get soft thresholds to use... |
| project_new_data | Project multicellular patterns to get scores on new data |
| reduce_dimensions | Gets a conos object of the data, aligning datasets across a... |
| reduce_to_vargenes | Reduce each cell type's expression matrix to just the... |
| render_multi_plots | Create a figure of all loadings plots arranged |
| reshape_loadings | Reshape loadings for a factor from linearized to matrix form |
| run_fgsea | Run fgsea for one cell type of one factor |
| run_gsea_one_factor | Run gsea separately for all cell types of one specified... |
| run_hypergeometric_gsea | Compute enriched gene sets among significant genes in a cell... |
| run_jackstraw | Run jackstraw to get genes that are significantly associated... |
| run_stability_analysis | Test stability of a decomposition by subsampling or... |
| run_tucker_ica | Run the Tucker decomposition and rotate the factors |
| sample_fibers | Get a list of tensor fibers to shuffle |
| scale_fontsize | Scale font size. From simplifyEnrichment package.... |
| scale_variance | Scale variance across donors for each gene within each cell... |
| seurat_to_scMinimal | Convert Seurat object to scMinimal object. Generally, this... |
| shuffle_fibers | Shuffle elements within the selected fibers |
| stack_tensor | Create the tensor object by stacking each pseudobulk cell... |
| stop_wrap | Helper function from simplifyEnrichment package.... |
| subset_scMinimal | Subset an scMinimal object by specified genes, donors, cells,... |
| test_container | Data container for testing tensor formation steps |
| tucker_ica_helper | Helper function for running the decomposition. Use the... |
| update_params | Update any of the experiment-wide parameters |
| vargenes_anova | Compute significantly variable genes via anova. Generally,... |
