| Artist |
Visualization Artist for Custom Plots |
| available_ele |
Extract Unique Elements from a Column with Optional Filtering |
| available_tissue_class |
Retrieve Available Tissue Classes for a Given Species |
| available_tissue_type |
Retrieve Available Tissue Types for a Given Species |
| check_marker |
Verify and Explore Cell Type Annotations |
| CHOL_DEGs |
Example DEGs data from Limma-Voom workflow for TCGA-CHOL project |
| dgeList |
Construct a DGEList Object (Deprecated) |
| dge_list |
Construct a DGEList Object |
| dprocess_dgeList |
Filter and Normalize DGEList Data (Deprecated) |
| finsert |
Create a Vector from an Index-to-Label Map |
| get_attr |
Retrieve Attributes from an R Object |
| get_marker |
Retrieve Markers for Specific Cells from cellMarker3 |
| groupStat |
Summarize Data by Group Using Regular Expressions (Deprecated) |
| groupStatI |
Summarize Data by Group Using an Index (Deprecated) |
| group_stat |
Perform Summary Analysis by Group Using Regular Expressions |
| group_stat_i |
Perform Summary Analysis by Group Using an column Index |
| limmaFit |
Fit a Linear Model for RNA-seq Data (Deprecated) |
| limma_fit |
Fit a Linear Model for RNA-seq data using limma |
| list2dt |
Convert a List with Vector Values to a Long Data.table |
| list2graph |
Convert a Named List into a Graph Based on Overlap |
| matchCellMarker2 |
Annotate Clusters by Matching Markers (Deprecated) |
| match_ref |
Annotate Clusters by Matching Markers with the CellMarker 3.0 Database |
| pbmc.markers |
Example marker data from Seurat::FindAllMarkers() |
| plotEnrichment2 |
Plot Enrichment for a Pathway (Deprecated) |
| plotGSEA |
Visualize GSEA Results (Deprecated) |
| plotMarkerDistribution |
Plot Distribution of a Marker (Deprecated) |
| plotORA |
Visualize ORA Test Results (Deprecated) |
| plotPossibleCell |
Plot Possible Cell Distribution (Deprecated) |
| plotRank |
Visualize GSEA Rank Statistics (Deprecated) |
| plotSeuratDot |
Create a Dot Plot of Marker Gene Expression (Deprecated) |
| plotVolcano |
Plot a Volcano Plot (Deprecated) |
| plot_enrichment |
Plot Enrichment for a Specific Pathway in fgsea |
| plot_gsea |
Visualization of GSEA Result from 'fgsea::fgsea()' |
| plot_marker_distribution |
Plot Distribution of a Marker Across Tissues and Cell Types |
| plot_ora |
Visualization of ORA Test Results |
| plot_possible_cell |
Plot Possible Cell Distribution Based on match_ref() Results |
| plot_rank |
Visualization of GSEA Rank Statistics |
| plot_seurat_dot |
Create a Dot Plot to Visualize Marker Gene Expression |
| plot_volcano |
Plot Volcano Plot for Differentially Expressed Genes |
| prepare_geo |
Download and Process GEO Data |
| prepare_tcga |
Prepare TCGA Data for Analysis |
| process_dge_list |
Filter Low-Expressed Genes and Normalize DGEList Data |
| setcolnames |
Rename Column Names (Deprecated) |
| setrownames |
Rename Row Names (Deprecated) |
| setSavedir |
Set a Directory for Saving Files (Deprecated) |
| set_colnames |
Rename Column Names of a Data Frame or Matrix |
| set_rownames |
Rename Row Names of a Data Frame or Matrix |
| set_savedir |
Set a Directory for Saving Files |
| split_matrix |
Split a Matrix into Smaller Sub-matrices by Column or Row |
| suggest_best_match |
Suggest Best Matches for a String from a Vector of Choices |
| theme_publication |
Custom ggplot2 Theme for Academic Publications |
| tuneParameters |
Tune Parameters for Cell Type Annotation (Deprecated) |
| tune_parameters |
Optimize Resolution and Gene Number Parameters for Cell Type Annotation |
| uniprot_id_map |
Map UniProt IDs to Other Identifiers |
| workIn |
Perform Operations in a Directory (Deprecated) |
| work_in |
Perform Operations in a Specified Directory and Return to the Original Directory |
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