harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data
Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.
| Version: | 1.2.4 |
| Depends: | R (≥ 3.5.0), Rcpp |
| Imports: | dplyr, cowplot, ggplot2, Matrix, methods, tibble, rlang, RhpcBLASctl |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress |
| Suggests: | SingleCellExperiment, Seurat (≥ 4.1.1), testthat, knitr, rmarkdown, ggthemes, ggrepel, patchwork, tidyverse, tidyr, data.table |
| Published: | 2025-10-10 |
| DOI: | 10.32614/CRAN.package.harmony |
| Author: | Ilya Korsunsky 
[cre, aut],
Martin Hemberg
[aut],
Nikolaos Patikas
[aut, ctb],
Hongcheng Yao
[aut, ctb],
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 |
| 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_1.2.4.tar.gz |
| Windows binaries: | r-devel: harmony_1.2.4.zip, r-release: harmony_1.2.4.zip, r-oldrel: harmony_1.2.4.zip |
| macOS binaries: | r-release (arm64): harmony_1.2.4.tgz, r-oldrel (arm64): harmony_1.2.4.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, Platypus, Seurat, singleCellTK, SVP |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=harmony to link to this page.