harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data
Implementation of the Harmony algorithm for single cell integration, described in Patikas, Yao, et al. <doi:10.64898/2026.03.16.711825>. Package includes a standalone Harmony function and interfaces to external frameworks.
| Version: | 2.0.2 |
| Depends: | R (≥ 4.2.0), Rcpp |
| Imports: | dplyr, cowplot, ggplot2, Matrix, methods, tibble, rlang, RhpcBLASctl, cli |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress |
| Suggests: | SingleCellExperiment, Seurat (≥ 4.1.1), testthat, knitr, rmarkdown, ggthemes, ggrepel, patchwork, tidyverse, tidyr, data.table |
| Published: | 2026-04-25 |
| DOI: | 10.32614/CRAN.package.harmony |
| Author: | Nikolaos Patikas 
[aut, ctb],
Hongcheng Yao
[aut, ctb],
Ilya Korsunsky
[cre, aut],
Martin Hemberg
[aut],
Nghia Millard
[aut],
Jean Fan [aut,
ctb],
Kamil Slowikowski
[aut, ctb],
Miles Smith [ctb],
Soumya Raychaudhuri
[aut] |
| Maintainer: | Ilya Korsunsky <ilya.korsunsky at gmail.com> |
| License: | GPL-3 |
| URL: | https://github.com/immunogenomics/harmony, https://pati-ni.github.io/harmony/ |
| NeedsCompilation: | yes |
| Materials: | NEWS |
| CRAN checks: | harmony results |
Documentation:
| Reference manual: | harmony.html , harmony.pdf |
| Vignettes: |
Using harmony in Seurat (source, R code) Detailed Walkthrough of Harmony Algorithm (source, R code) Quick start to Harmony (source, R code) |
Downloads:
| Package source: | harmony_2.0.2.tar.gz |
| Windows binaries: | r-release: harmony_2.0.2.zip, r-oldrel: harmony_1.2.4.zip |
| macOS binaries: | r-release (arm64): harmony_2.0.2.tgz, r-oldrel (arm64): harmony_2.0.2.tgz, r-release (x86_64): harmony_1.2.4.tgz, r-oldrel (x86_64): harmony_1.2.4.tgz |
| Old sources: | harmony archive |
Reverse dependencies:
| Reverse imports: | clustSIGNAL, lemur, PRECAST, ProFAST, RaceID, scAnnotate, SCdeconR, symphony |
| Reverse suggests: | Banksy, Seurat, singleCellTK, SVP |
Linking:
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