Package index • RightOmicsTools

Seurat

Visualization

Barplot_Cell_Proportion(): Bar plot of the cell proportions in each identity

DotPlot_Heatmap(): Dot plot or heatmap of average gene expression in each identity

Cell_Heatmap(): Heatmap of gene expression in each cell

Grid_VlnPlot(): Square stacked violin plot of gene expression in each identity

Helper Functions

Right_DietSeurat(): Reduce the size of a Seurat object

GSEA_Signatures(): Gene signatures from GSEA-MSigDB pathways

Find_Annotation_Markers(): Get the top markers for fast annotation

tradeSeq

Visualization

curveSmoothers(): Scatterplot of log-transformed counts, and average fitted GAM smoother curves along pseudotime

heatmapSmoothers(): Heatmap of average fitted GAM smoothers along pseudotime

Helper Functions

tradeSeqPreprocess(): Remove genes with very low expression for tradeSeq analysis

tradeSeqTests(): Perform tradeSeq tests in parallel

CIBERSORTx

Reference_Matrix_Builder(): Builder of CIBERSORTx Reference Matrix

Mixture_File_Builder(): Builder of CIBERSORTx Mixture File

Data

Right_Data(): Data loader for vignettes

ncRNA_human: Human non-coding genes

pseudogenes_mouse: Mouse pseudogenes