Man pages for scITD
Single-Cell Interpretable Tensor Decomposition

apply_combatApply ComBat batch correction to pseudobulk matrices....
calculate_fiber_fstatsCalculate F-Statistics for the association between donor...
check_rec_presHelper function to check whether receptor is present in...
clean_dataClean data to remove genes only expressed in a few cells and...
colMeanVarsCalculates column mean and variance. Adapted from pagoda2....
compare_decompositionsPlot a pairwise comparison of factors from two separate...
compute_associationsCompute associations between donor proportions and factor...
compute_donor_propsGet donor proportions of each cell type or subtype
compute_LR_interactCompute and plot the LR interactions for one factor
convert_gnConvert gene identifiers to gene symbols
determine_ranks_tuckerRun rank determination by svd on the tensor unfolded along...
form_tensorForm the pseudobulk tensor as preparation for running the...
get_all_lds_factor_plotsGenerate loadings heatmaps for all factors
get_callouts_annotGet gene callout annotations for a loadings heatmap
get_ctype_exp_varGet explained variance of the reconstructed data using one...
get_ctype_prop_associationsCompute and plot associations between donor factor scores and...
get_ctype_subc_prop_associationsCompute and plot associations between donor factor scores and...
get_ctype_vargenesPartition main gene by cell matrix into per cell type...
get_donor_metaGet metadata matrix of dimensions donors by variables (not...
get_factor_exp_varGet the explained variance of the reconstructed data using...
get_fstats_pvalsCalculate adjusted p-values for gene_celltype fiber-donor...
get_gene_modulesCompute WGCNA gene modules for each cell type
get_gene_set_vectorsGet logical vectors indicating which genes are in which...
get_indv_subtype_associationsCompute subtype proportion-factor association p-values for...
get_intersecting_pathwaysExtract the intersection of gene sets which are enriched in...
get_leading_edge_genesGet the leading edge genes from GSEA results
get_lm_pvalsCompute gene-factor associations using univariate linear...
get_max_correlationsComputes the max correlation between each factor of the...
get_meta_associationsGet metadata associations with factor donor scores
get_min_sig_genesEvaluate the minimum number for significant genes in any...
get_module_enrIdentify gene sets that are enriched within specified gene...
get_normalized_varianceGet normalized variance for each gene, taking into account...
get_num_batch_ranksPlot factor-batch associations for increasing number of donor...
get_one_factorGet the donor scores and loadings matrix for a single-factor
get_pseudobulkCollapse data from cell-level to donor-level via summing...
get_real_fstatsGet F-Statistics for the real (non-shuffled) gene_ctype...
get_reconstruct_errors_svdCalculate reconstruction errors using svd approach
get_significance_vectorsGet vectors indicating which genes are significant in which...
get_subclust_de_hmapsGet list of cell subtype differential expression heatmaps
get_subclust_enr_dotplotGet scatter plot for association of a cell subtype proportion...
get_subclust_enr_figGet a figure showing cell subtype proportion associations...
get_subclust_enr_hmapGet heatmap of subtype proportion associations for each...
get_subclustersPerform leiden subclustering to get cell subtypes
get_subclust_umapGet a figure to display subclusterings at multiple...
get_subtype_prop_associationsCompute and plot associations between factor scores and cell...
get_sumsCalculates factor-stratified sums for each column. Adapted...
ht_clustersVisualize the similarity matrix and the clustering. Adapted...
identify_sex_metadataExtract metadata for sex information if not provided already
initialize_paramsInitialize parameters to be used throughout scITD in various...
instantiate_scMinimalCreate an scMinimal object. Generally, this should be done...
make_new_containerCreate a container to store all data and results for the...
merge_small_clustsMerge small subclusters into larger ones
nmf_unfoldedComputes non-negative matrix factorization on the tensor...
normalize_countsHelper function to normalize and log-transform count data
normalize_pseudobulkNormalize the pseudobulked counts matrices. Generally, this...
norm_var_helperCalculates the normalized variance for each gene. This is...
parse_data_by_ctypesParse main counts matrix into per-celltype-matrices....
pca_unfoldedComputes singular-value decomposition on the tensor unfolded...
plotDEheatmap_conosPlot a heatmap of differential genes. Code is adapted from...
plot_donor_matrixPlot matrix of donor scores extracted from Tucker...
plot_donor_propsPlot donor celltype/subtype proportions against each factor
plot_donor_sig_genesGenerate a gene by donor heatmap showing scaled expression of...
plot_dscore_enrCompute enrichment of donor metadata categorical variables at...
plot_gsea_hmapPlot enriched gene sets from all cell types in a heatmap
plot_gsea_hmap_w_similarityPlot already computed enriched gene sets to show semantic...
plot_gsea_subLook at enriched gene sets from a cluster of semantically...
plot_loadings_annotPlot the gene by celltype loadings for a factor
plot_mod_and_ligPlot trio of associations between ligand expression, module...
plot_multi_module_enrGenerate gene set x ct_module heatmap showing co-expression...
plot_rec_errors_bar_svdPlot reconstruction errors as bar plot for svd method
plot_rec_errors_line_svdPlot reconstruction errors as line plot for svd method
plot_scores_by_metaPlot dotplots for each factor to compare donor scores between...
plot_select_setsPlot enrichment results for hand picked gene sets
plot_stability_resultsGenerate a plot for either the donor scores or loadings...
plot_subclust_associationsPlot association significances for varying clustering...
prep_LR_interactPrepare data for LR analysis and get soft thresholds to use...
reduce_dimensionsGets a conos object of the data, aligning datasets across a...
reduce_to_vargenesReduce each cell type's expression matrix to just the...
render_multi_plotsCreate a figure of all loadings plots arranged
reshape_loadingsReshape loadings for a factor from linearized to matrix form
run_fgseaRun fgsea for one cell type of one factor
run_gsea_one_factorRun gsea separately for all cell types of one specified...
run_hypergeometric_gseaCompute enriched gene sets among significant genes in a cell...
run_jackstrawRun jackstraw to get genes that are significantly associated...
run_stability_analysisTest stability of a decomposition by subsampling or...
run_tucker_icaRun the Tucker decomposition and rotate the factors
sample_fibersGet a list of tensor fibers to shuffle
scale_fontsizeScale font size. From simplifyEnrichment package....
scale_varianceScale variance across donors for each gene within each cell...
seurat_to_scMinimalConvert Seurat object to scMinimal object. Generally, this...
shuffle_fibersShuffle elements within the selected fibers
stack_tensorCreate the tensor object by stacking each pseudobulk cell...
stop_wrapHelper function from simplifyEnrichment package....
subset_scMinimalSubset an scMinimal object by specified genes, donors, cells,...
test_containerData container for testing tensor formation steps
tucker_ica_helperHelper function for running the decomposition. Use the...
tucker_sparseTucker Decomposition adapted from rTensor but with sparsity...
update_paramsUpdate any of the experiment-wide parameters
vargenes_anovaCompute significantly variable genes via anova. Generally,...
scITD documentation built on Nov. 4, 2021, 1:06 a.m.