Single Cell Mapper


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Documentation for package ‘scMappR’ version 0.1.3

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cellmarker_enrich Fisher's Exact Cell-Type Identification.
coEnrich Identify co-expressed cell-types
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 matrix.
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 gprofileR Barplot (TF)
pathway_enrich_internal Pathway enrichment for cellWeighted_Foldchange's 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_Foldchange, 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