Man pages for vallotlab/IDclust
Iterative Differential Clustering for single-cell
| add_gene_to_DA_list | Add genes to differential analysis using a... |
| calculate_FalseNegative | Calculate False Negative markers for SingleCellExperiment... |
| calculate_FalsePositive | Calculate False Positives markers for SingleCellExperiment... |
| create_pseudobulk_mat | Create Pseudo-Bulk Matrice from scRNA clusters & replicates |
| create_pseudobulk_mat.default | Create Pseudo-Bulk Matrix from scEpigenomics clusters &... |
| create_pseudobulk_mat.Seurat | Create Pseudo-Bulk Matrice from scRNA clusters & replicates |
| differential_ChromSCape | Differential analysis with ChromSCape (differential... |
| differential_edgeR_pseudobulk_LRT | Pseudo-bulk differential analysis with edgeR (LRT) |
| differential_edgeR_pseudobulk_LRT.default | Pseudo-bulk differential analysis with edgeR (LRT) |
| differential_edgeR_pseudobulk_LRT.Seurat | Pseudo-bulk differential analysis with edgeR (LRT) |
| differential_pathway | Find differential pathways with enrichR |
| differential_Seurat | Differential function Seurat (wilcoxon) |
| find_differentiated_clusters | Find Differentiated Clusters |
| IDC_DA_scEpigenomics | A data.frame containing the differential markers for... |
| IDC_DA_scRNA | A data.frame containing the differential markers for scRNA... |
| IDC_summary_scEpigenomics | A data.frame containing the summary of differential markers... |
| IDC_summary_scRNA | A data.frame containing the summary of differential markers... |
| iterative_differential_clustering | iterative_differential_clustering |
| lm_list | A list of linear models of false positive differential... |
| plot_cluster_network | Plot Iterative Differential Clustering network |
| processing_ChromSCape | Normalize and run PCA with ChromSCape (LSI) |
| processing_Seurat | Normalize and run PCA with Seurat |
| scExp | A SingleCellExperiment object containing the scH3K27ac part... |
| Seu | A Seurat object containing the scRNA part of Paired-Tag... |
| summarise_DA | Summarise Differential Analysis table |
| top_differential_markers | Retrieve top marker genes from list of differential analysis |
| top_enriched_pathways | Find enriched pathways in marker genes of IDclust |
