R Observatory: Metrics for harmony version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

harmony

2.0.5

Fast, Sensitive, and Accurate Integration of Single Cell Data

3packages depend

243.7Kdownloads / year

66.2%test coverage

13/13checks pass

Overview

About

Maintained by Ilya KorsunskyFirst published 2021-06-0213 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("harmony", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("immunogenomics/harmony")

Development version from immunogenomics/harmony. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-harmony

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-harmony

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-harmony

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 7.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.13

66.2%

Coverage · measured lines

67%

Documentation · exports

10

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-19
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-18
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-07-03
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 9 earlier snapshots

ERROR2026-06-27
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-13
9 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-14
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
7 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 60%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

243.7K

CRAN downloads in the past year

Rank #763 · ~668/day · ~20.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

21.6K30 days

66.7K90 days

243.7K1 year

Compare downloads with other packages →

Also on3.1K r2u18 autocran23.8K conda_forge1.4K bioconda

Repository

GitHub ↗ immunogenomics/harmony

667Stars

109Forks

82Open issues

2Open PRs

1Releases

416Commits

14Contributors

scrna-seqalgorithmdata-integrationr

416 commits · Last activity 2026-06-05 · +0.3% stars, 30d

Stars over time

2026-07-14 · 6652026-08-02 · 667

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/immunogenomics/harmony on 2026-08-16.

Continuous integration (2)

Travis CIAppVeyor

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.2.0Rcpp

Imports (9)

dplyr cowplot ggplot2Matrixmethodstibble rlang RhpcBLASctl cli

LinkingTo (3)

Rcpp RcppArmadillo RcppProgress

Suggests (11)

SingleCellExperiment Seurat testthat knitr rmarkdown ggthemes ggrepel patchwork tidyverse tidyr data.table

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

RaceID ProFAST Seurat

Code & Tests

People & History

People (9)

Maintainer (1)

Ilya Korsunsky

Maintainer, Author

Authors (8)

Ilya Korsunsky

Maintainer, Author

Jean Fan

Author, Contributor

Martin Hemberg

Author · added in 1.2.1

Nghia Millard

Author

Nikolaos Patikas

Author, Contributor · added in 1.2.1

Soumya Raychaudhuri

Author

Kamil Slowikowski

Author, Contributor

Hongcheng Yao

Author, Contributor · added in 1.2.1

Contributors (5)

Jean Fan

Author, Contributor

Nikolaos Patikas

Author, Contributor · added in 1.2.1

Kamil Slowikowski

Author, Contributor

Hongcheng Yao

Author, Contributor · added in 1.2.1

Miles Smith

Contributor

Package Timeline

13 releases. Pick two to compare their code metrics. R releases are shown for context.

2.0.5Latest
2026-06-13 · current release · diff ↗
unarchivedReturned to CRAN
2026-06-13
archivedRemoved from CRAN
2026-06-11
issues were not corrected in time
2.0.4
2026-06-04 · diff ↗
2.0.3
2026-05-13 · diff ↗
2.0.2
2026-04-25 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.2.4
2025-10-10 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.3
2024-11-28 · diff ↗
1.2.1
2024-08-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
2023-11-29 · diff ↗
1.1.0
2023-10-23 · diff ↗
1.0.3
2023-10-01 · diff ↗
1.0.1
2023-09-20 · diff ↗

Show 7 earlier events

R
R 4.3.0 released · 2023-04-21
0.1.1
2022-11-14 · diff ↗
unarchivedReturned to CRAN
2022-11-14
archivedRemoved from CRAN
2022-10-30
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
0.1.0
2021-06-02
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-02
Total releases: 13 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.2.0
Bundled data: 2.9 MB / 3 files
Download size: 5.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("harmony")

Format

Korsunsky, I., Fan, J., Hemberg, M., Millard, N., Patikas, N., Raychaudhuri, S., Slowikowski, K., Smith, M., & Yao, H. (2026). harmony: Fast, Sensitive, and Accurate Integration of Single Cell Data (Version 2.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.harmony

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for harmony version 2.0.5 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →