Package: harmony 2.0.3

Ilya Korsunsky

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.

Authors: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]

harmony_2.0.3.tar.gz
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harmony_2.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
harmony/json (API)
NEWS

# Install 'harmony' in R:
install.packages('harmony', repos = c('https://immunogenomics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immunogenomics/harmony/issues

Pkgdown/docs site:https://pati-ni.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • cell_lines - List of metadata table and scaled PCs matrix
  • 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.
  • 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.

On CRAN:

Conda:

algorithmdata-integrationscrna-seqopenblascpp

15.17 score 650 stars 11 packages 11k scripts 22k downloads 6 mentions 3 exports 32 dependencies

Last updated from:bad0f15852. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK234
linux-devel-x86_64OK295
source / vignettesOK371
linux-release-arm64OK230
linux-release-x86_64OK229
macos-release-arm64OK123
macos-release-x86_64OK271
macos-oldrel-arm64OK121
macos-oldrel-x86_64OK335
windows-develOK245
windows-releaseOK203
windows-oldrelOK264
wasm-releaseOK149

Exports:%>%harmony_optionsRunHarmony

Dependencies:clicowplotcpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMatrixpillarpkgconfigR6RColorBrewerRcppRcppArmadilloRcppProgressRhpcBLASctlrlangS7scalestibbletidyselectutf8vctrsviridisLitewithr

Detailed Walkthrough of Harmony Algorithm

Korsunsky et al.: Fast, sensitive, and accurate integration of single cell data with Harmony

Rendered fromdetailedWalkthrough.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-05
Started: 2023-09-20

Quick start to Harmony

Rendered fromquickstart.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-05
Started: 2019-04-16

Using harmony in Seurat

Rendered fromSeurat.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2026-05-05
Started: 2023-09-20