Man pages for altairwei/rhapsodykit
A Set of Tools for BD Rhapsody WTA Downstream Analysis
| barplot_cluster_abundance | Plot Abundance Comparison Across Sample Clusters |
| calculateClusterProportion | Calculate the percentage of cell types in samples |
| calculate_pseudo_bulk | Calculate pseudo-bulk RNA-Seq data from scRNA-Seq. |
| diff_state_apply | Apply funtion on each data.frame of differential state... |
| diff_state_filter | Filter differential state analysis results. |
| diff_state_format | Format differential state testing results into an easily... |
| diff_state_pull | Pull out column from diff state results. |
| diff_state_ranked_lfc | Prepare ranked logFC vector named with gene names. |
| diff_state_significant | Filter differential state analysis results by FDR and logFC. |
| diff_state_significant_lfc | Prepare significant logFC vector named with gene names. |
| diff_state_subset | Subset Differential State Results |
| diff_state_summary | Summarize results from differential state analysis. |
| expr_freq_filter | Filter differential state analysis results by gene expression... |
| fetch_cellular_data | Access Cellular Data from SeuratDisk File |
| find_all_avg_expr_genes | Generate average expression of different sample for all cell... |
| find_all_conserved_markers | Find conserved markers for all cell identity classes |
| find_all_diff_expr_genes | Find differential expressed genes on variable conditions for... |
| findDACombinedClusters | Combine differential abundant subpopulation |
| findDiffAbundantCells | Run DAseq algorithm |
| findDiffAbundantMarkers | Find markers for differential abundant subpopulation |
| find_group_marker_genes | Find group-specific genes. |
| from_list_to_upset | List of vectors to UpSet data converter |
| genecount_diff_state | Plot number of genes per subpopulation per contrast. |
| generate_seurat_plots | Generate plots with the Seurat object |
| heatmap_cross_sample | Plot heatmap across samples. |
| integrated_sample_analysis | Perform Seurat integrated analysis for grouped samples |
| integration_analysis | Perform general Seurat analysis on integrated object |
| integration_anchorset | Get integration anchorset from Seurat objects. |
| intersection_counts | Query element counts of intersections. |
| key_mapping | Mapping key according to a given dict. |
| make_integrated_pseudo_bulk | Make pseudo-bulk RNA-Seq data from a Seurat object. |
| make_pseudo_bulk | Make pseudo-bulk RNA-Seq from scRNA-Seq. |
| merge_sample | Merge Seurat objects into one without batch effect correction |
| onlyDAscore | Calculate DA Score |
| perform_diff_gene | Perform differentially expressed genes analysis. |
| perform_find_all_markers | Find gene markers for all cell identity classes |
| pipe | Pipe operator |
| plot_avg_expr_genes | Plot scatter diagram to compare average expression value of... |
| plotDACellLabel | DA subpopulation clustering result is shown in the 2D... |
| plotDACellScore | Plot DA Cell Scores |
| plotDAEmbedding | Plot DA Embedding |
| plotDAOverlap | Plot the Overlap Between Cell Type and DA Subpopulations |
| plotDARandomPermutation | Plot the Random Permutation of DA Measure |
| plotDASite | Selected DA cells are highlighted in the 2D embedding |
| prepare_muscat_sce | Prepare SingleCellExperiment object for muscat package. |
| pseudobulk_diff_state | Perform differential state analysis on pseudo-bulk data. |
| read_expression_st | Each row records counts for cell-gene combinations that have... |
| read_molecules_csv | Read raw expression matrix from Rhapsody WTA pipeline |
| read_mols_per_cell | Each row represents the number of molecules in a cell for... |
| read_mtx | Read 'Matrix' data from cached folder. |
| read_rhapsody_wta | Read expression data from results folder of Rhapsody WTA... |
| read_unfiltered_csv | Read unfiltered expression matrix from Rhapsody WTA pipeline |
| reassign_sample | Reassign sample name. |
| save_expression_matrix | Save Matrix data to disk. |
| save_plot | Wrapper for 'ggsave' with more messages. |
| save_to_disk | Save Single-Cell Object to Disk |
| single_sample_analysis | Perform single sample Seurat analysis |
| upset_dataframe | Convert UpSet binary data to tidy data.frame |
| upset_plot | Plot UpSet diagram from tidy UpSet data.frame |
| upset_updown_regulated | Plot up/down-regulated genes in one diagram |
| volcano_diff_state | Volcano plot for differential state analysis. |
