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

## 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