Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference

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Documentation for package ‘SCdeconR’ version 1.0.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

bulk_generator	Generate artificial bulk RNA-seq samples based on simulation
celltype_expression	Compute cell type specific gene expression
comparedeg_scatter	Generate a scatter plot comparing two differential expression results
comparegsea_scatter	Generate a scatter plot comparing two gene set enrichment analysis results
compute_metrics	Statistical evaluations of predicted cell proportions
construct_ref	Integration of single-cell/nuclei RNA-seq data as reference
gsea_heatmap	Heatmap to demonstrate enrichment of selected gene-sets
gsea_rwplot	GSEA random-walk plot
gsea_sumplot	Summary plot of gene set enrichment analysis
load_scdata	Load, filter and normalize scRNA-seq/snRNA-seq data
prepare_rnk	Prepare .rnk file for GSEA preranked analysis
prop_barplot	Bar plot of cell type proportions across samples
read_gmt	Methods to manipulate .gmt files
reformat_gmt	Methods to manipulate .gmt files
run_de	Differential expression analysis
scaling	Normalization of gene expression data
scdecon	Deconvolution of bulk RNA-seq data
transformation	Transformation of gene expression data
write_gmt	Methods to manipulate .gmt files