single-cell-RNA-seq

Functions for single-cell and single-nucleus RNA-Seq analyses.

Differential expression

pseudobulk: Generate pseudobulk data per cell type or cluster from a Seurat object

runLimmaPseudobulked: Differential expression by cell type or cluster using limma with pseudobulk data

runLimmaDream: Differential expression by cell type or cluster using limma with dream to enable mixed model (1|sample)

runRoast: wrapper for ROAST pathway analysis using output from runLimmaPseudobulked

runCamera: wrapper for Camera pathway analysis using output from runLimmaPseudobulked

plotVolcano: make volcano plots from output of runLimmaPseudobulked or runLimmaDream

makeContrastScatter: scatterplot comparing logFC of genes in one contrast vs another contrast within cell type

Cell-cell communication ligand-receptor analysis

runNicheNetR: wrapper for NicheNetR ligand-receptor analysis that produces numerous summary plots and tables

makeCircos: make Circos plots from output of runNichNetR()

Coming soon:

1. wrapper function to import CellRanger output and organize for Seurat
2. Example workflow