Man pages for ConesaLab/acorde
Isoform co-usage networks from single-cell RNA-seq data
| calculate_cluster_ctmeans | Calculate isoform-level summary metrics for a cluster |
| calculate_cluster_profile | Calculate mean profile of an isoform cluster |
| cell_type_DE | Test differential expression of isoforms across cell types |
| check_gene_pair | Check isoform co-expression patterns for a gene pair across... |
| cluster_isoforms | Initial clustering of isoforms using dynamicTreeCut |
| consensus_DE_set | Isoform Differential Expression analysis results |
| detect_low_expression | Filter isoforms by absolute expression level across cell... |
| detect_minor_isoforms | Filter isoforms by gene-relative expression across cell types |
| detect_sparse | Filter isoforms by maximum cell type-level proportion of... |
| expand_clusters | Expand clusters with unclustered isoforms |
| filter_clusters | Remove isoforms with low correlation from clusters |
| find_codiu_genes | Detect genes with co-Differential Isoform Usage |
| fromList | Obtaining intersections from a list of named vectors |
| gene_tr_ID | Gene-isoform associations for the mouse neural long read... |
| keep_DIU | Keep isoforms from genes with Differential Isoform Usage... |
| make_design | Create design matrix for co-DIU test of a pair of genes |
| make_test | Perform co-DIU statistical test for one gene pair |
| merge_clusters | Merge redundant clusters by expression profile similarity |
| metadata | Tasic et al. 2016 metadata |
| percentile_cor | Compute percentile correlations between a set of transcripts |
| percentile_expr | Summarize cell type-level expression using percentiles |
| plot_cluster_ctmeans | Plot cell type expression of all isoforms in a cluster |
| plot_cluster_profile | Plot mean profile of an isoform cluster |
| run_downsampling | Run one downsampling iteration on Tasic et al. dataset |
| scale_isoforms | Scale single-cell expression data for cluster visualization |
| shuffle_group_matrix | Reorder cell type-specific expression matrix during... |
| simulate_coexpression | Simulate co-expression patterns on an already-simulated... |
| symsim_sce | SymSim simulated dataset |
| tasic | Tasic et al. 2016 expression matrix |
| test_codiu_genes | Statistical testing of candidate co-DIU genes |
