Reference

All functions

RunHarmony()

Generic function that runs the harmony algorithm on single-cell genomics cell embeddings.

RunHarmony(<Seurat>)

Applies harmony on a Seurat object cell embedding.

RunHarmony(<SingleCellExperiment>)

Applies harmony on PCA cell embeddings of a SingleCellExperiment.

RunHarmony(<default>)

This is the primary harmony interface.

cell_lines

List of metadata table and scaled PCs matrix

cell_lines_small

Same as cell_lines but smaller (300 cells).

harmony_options()

Set advanced parameters for RunHarmony

pbmc.ctrl

Gene expression data of control PBMC from Kang et al. 2017. This contains a sample of 1000 cells from that condition and is used for the Seurat Vignette.

pbmc.stim

Gene expression data of stimulated PBMC from Kang et al. 2017. This contains a sample of 1000 cells from that condition and is used for the Seurat Vignette.