Fast, Sensitive, and Accurate Integration of Single Cell Data

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Documentation for package ‘harmony’ version 1.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

cell_lines	List of metadata table and scaled PCs matrix
cell_lines_small	Same as cell_lines but smaller (300 cells).
harmony	Harmony: fast, accurate, and robust single cell integration.
HarmonyMatrix	A proxy call to 'RunHarmony()'. Deprecated.
harmony_options	Set advanced options for RunHarmony
moe_ridge_get_betas	Get beta Utility
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.
RunHarmony	Generic function that runs the harmony algorithm on single-cell genomics cell embeddings.
RunHarmony.default	This is the primary harmony interface.
RunHarmony.Seurat	Applies harmony on a Seurat object cell embedding.
RunHarmony.SingleCellExperiment	Applies harmony on PCA cell embeddings of a SingleCellExperiment.