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harmony (version 2.0.5)

Fast, Sensitive, and Accurate Integration of Single Cell Data

Description

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

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Install

install.packages('harmony')

Monthly Downloads

23,919

Version

2.0.5

License

GPL-3

Issues

82

Pull Requests

2

Stars

665

Forks

110

Maintainer

Ilya Korsunsky

Last Published

June 12th, 2026

Functions in harmony (2.0.5)

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.
harmony_options

Set advanced parameters for RunHarmony
RunHarmony.Seurat

Applies harmony on a Seurat object cell embedding.
RunHarmony.default

This is the primary harmony interface.
RunHarmony.SingleCellExperiment

Applies harmony on PCA cell embeddings of a SingleCellExperiment.
cell_lines

List of metadata table and scaled PCs matrix
%>%

Pipe operator
harmony

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

Same as cell_lines but smaller (300 cells).
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.