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harmony (version 1.2.4)

Fast, Sensitive, and Accurate Integration of Single Cell Data

Description

Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al . Package includes a standalone Harmony function and interfaces to external frameworks.

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Install

install.packages('harmony')

Monthly Downloads

23,735

Version

1.2.4

License

GPL-3

Issues

79

Pull Requests

2

Stars

600

Forks

105

Maintainer

Ilya Korsunsky

Last Published

October 10th, 2025

Functions in harmony (1.2.4)

harmony

Harmony: fast, accurate, and robust single cell integration.
RunHarmony

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

Get beta Utility
HarmonyMatrix

A proxy call to RunHarmony(). Deprecated.
harmony_options

Set advanced parameters for RunHarmony
RunHarmony.SingleCellExperiment

Applies harmony on PCA cell embeddings of a SingleCellExperiment.
RunHarmony.Seurat

Applies harmony on a Seurat object cell embedding.
cell_lines_small

Same as cell_lines but smaller (300 cells).
RunHarmony.default

This is the primary harmony interface.
cell_lines

List of metadata table and scaled PCs matrix
%>%

Pipe operator
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.
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.