Artist | Visualization Artist for Custom Plots |
check_marker | Verify Markers for Specific Clusters Using matchCellMarker |
CHOL_DEGs | Example DEGs data from Limma-Voom workflow for TCGA-CHOL... |
dgeList | Construct a DGEList Object |
dprocess_dgeList | Filter Low-Expressed Genes and Normalize DGEList Data |
finsert | Insert Specific Values into a Character Vector at Defined... |
get_attr | Retrieve Attributes from an R Object |
get_marker | Retrieve Markers for Specific Cells from cellMarker2 |
groupStat | Perform Summary Analysis by Group Using Regular Expressions |
groupStatI | Perform Summary Analysis by Group Using an Index |
limmaFit | 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 | Match Markers with cellMarker2 Dataset |
pbmc.markers | Example marker data from Seurat::FindAllMarkers() |
plotEnrichment2 | Plot Enrichment for a Specific Pathway in fgsea |
plotGSEA | Visualization of GSEA Result from 'fgsea::fgsea()' |
plotMarkerDistribution | Plot Distribution of a Marker Across Tissues and Cell Types |
plotORA | Visualization of ORA Test Results |
plotPossibleCell | Plot Possible Cell Distribution Based on matchCellMarker2()... |
plotRank | Visualization of GSEA Rank Statistics |
plotSeuratDot | Create Dot Plots for Markers from check_marker |
plotVolcano | Plot Volcano Plot for Differentially Expressed Genes |
prepare_geo | Download and Process GEO Data |
prepare_tcga | Prepare TCGA Data for Analysis |
setcolnames | Rename Column Names of a Data Frame or Matrix |
setrownames | Rename Row Names of a Data Frame or Matrix |
setSavedir | Set a Directory for Saving Files |
split_matrix | Split a Matrix into Smaller Submatrices by Column |
theme_publication | Custom ggplot2 Theme for Academic Publications |
tuneParameters | Optimize Resolution and Gene Number Parameters for Cell Type... |
uniprot_id_map | Map UniProt IDs to Other Identifiers |
workIn | Perform Operations in a Specified Directory and Return to the... |
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