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 |