Fast, Sensitive, and Accurate Integration of Single Cell Data [R package harmony version 1.2.4]

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年10月10日

DOI: 10.32614/CRAN.package.harmony

Author: Ilya Korsunsky ORCID iD [cre, aut], Martin Hemberg ORCID iD [aut], Nikolaos Patikas ORCID iD [aut, ctb], Hongcheng Yao ORCID iD [aut, ctb], Nghia Millard ORCID iD [aut], Jean Fan ORCID iD [aut, ctb], Kamil Slowikowski ORCID iD [aut, ctb], Miles Smith [ctb], Soumya Raychaudhuri ORCID iD [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:

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