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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: 1.2.1
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: 2024-08-27
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.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_1.2.1.tar.gz
Windows binaries: r-devel: harmony_1.2.1.zip, r-release: harmony_1.2.1.zip, r-oldrel: harmony_1.2.1.zip
macOS binaries: r-release (arm64): harmony_1.2.1.tgz, r-oldrel (arm64): harmony_1.2.1.tgz, r-release (x86_64): harmony_1.2.1.tgz, r-oldrel (x86_64): harmony_1.2.1.tgz
Old sources: harmony archive

Reverse dependencies:

Reverse imports: lemur, ProFAST, RaceID, scAnnotate, SCdeconR, SCIntRuler, symphony
Reverse suggests: Banksy, Platypus, Seurat, singleCellTK

Linking:

Please use the canonical form https://CRAN.R-project.org/package=harmony to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.