R: Single Cell Mapper

# Single Cell Mapper

## Documentation for package ‘scMappR’ version 1.0.12

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

cellmarker_enrich | Fisher's Exact Cell-Type Identification.
coEnrich | Identify co-expressed cell-types
compare_deconvolution_methods | compare_deconvolution_methods
cwFoldChange_evaluate | Measure cell-type specificity of cell-weighted Fold-changes
DeconRNAseq_CRAN | DeconRNASeq CRAN compatible
deconvolute_and_contextualize | Generate cell weighted Fold-Changes (cwFold-changes)
extract_genes_cell | Extract Markers
generes_to_heatmap | Generate signature matrix
get_gene_symbol | Internal - get gene symbol from Panglao.db assigned gene-names (symbol-ensembl).
get_signature_matrices | Get signature matrices.
gmt | gmt_example
gProfiler_cellWeighted_Foldchange | Pathway enrichment for cwFold-changes
gsva_cellIdentify | Cell-type naming with GSVA
heatmap_generation | Generate Heatmap
human_mouse_ct_marker_enrich | Consensus cell-type naming (Fisher's Exact)
make_TF_barplot | Plot g:profileR Barplot (TF)
pathway_enrich_internal | Internal - Pathway enrichment for cellWeighted_Foldchanges and bulk gene list
PBMC_example | PBMC_scMappR
plotBP | Plot gProfileR Barplot
POA_example | Preoptic_Area
process_dgTMatrix_lists | Count Matrix To Signature Matrix
process_from_count | Count Matrix To Seurat Object
scMappR_and_pathway_analysis | Generate cellWeighted_Foldchanges, visualize, and enrich.
scMappR_tissues | scMappR_tissues
seurat_to_generes | Identify all cell-type markers
single_gene_preferences | Single cell-type gene preferences
sm | single_cell_process
tissue_by_celltype_enrichment | tissue_by_celltype_enrichment
tissue_scMappR_custom | Gene List Visualization and Enrichment with Custom Signature Matrix
tissue_scMappR_internal | Gene List Visualization and Enrichment (Internal)
tochr | To Character.
toNum | To Numeric.
topgenes_extract | Extract Top Markers
two_method_pathway_enrichment | two_method_pathway_enrichment