Single Cell Mapper

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Documentation for package ‘scMappR’ version 1.0.12

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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