Single-Cell Interpretable Tensor Decomposition

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,... |

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