R Observatory: Metrics for harmony version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

harmony

2.0.5Package record

Fast, Sensitive, and Accurate Integration of Single Cell Data

2packages dependsuggested by 2

238.5Kdownloads / year

66.2%test coverage

13/13flavors OK

Overview

About

Maintained by Ilya KorsunskyCRAN page ↗GitHub ↗Website ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-19
ERROR12 OK, 1 ERROR2026-07-18
OK13 OK2026-07-03

Show 9 earlier changesHide 9 earlier changes

ERROR12 OK, 1 ERROR2026-06-27
OK9 OK2026-06-13
ERROR12 OK, 1 ERROR2026-05-14
OK13 OK2026-05-02
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE8 OK, 6 NOTE2026-04-10
ERROR7 OK, 6 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.5

README· In the repository, left out of the releaseVignettesYes · 3 · dynamicNEWSYes · 67% structuredCitation fileNoWebsiteYes

Help pages: 11 (2 internal)includes a package overview page
Examples that run: 40%2 run in a plain check · 3 never run
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

238.5K

CRAN downloads in the past year

Rank #792 · ~653/day · ~19.9K/mo

Releases R versions

Daily download trend is not available in this view yet.

17K30 days

59.2K90 days

238.5K1 year

Compare downloads with other packages →

Also on5.6K r2u12 autocran28.3K conda_forge5.6K bioconda

How downloads are counted

Repository

immunogenomics/harmony ↗Organization: immunogenomics

677Stars

109Forks

83Open issues

4Open PRs

1Releases

422Commits

15Commit identities

scrna-seqalgorithmdata-integrationr

422 commits · Last activity 2026-10-15 · +0.7% stars, 30d · The default branch showed an older version (2.0.4) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 42
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 6652026-10-16 · 677

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/immunogenomics/harmony on 2026-10-11.

Continuous integration (2)

Travis CI (config file)AppVeyor

Docs source (1)

GitHub Pages site last deployed 2022-11-12

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing harmony adds 30 packages (15 with compiled code, 20 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, cowplot 1.6 MB.

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

2direct

1indirect

Imports 2

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

SCIntRuler RaceID

Suggests, most downloaded first

Seurat ProFAST

How these are counted

Code & Tests

Datasets

People & History

People (9)

Ilya Korsunsky

Maintainer since 0.1.0 (2021), 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

Miles Smith

Contributor

Releases (13)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-06-13
2.0.5Latest
record
2026-06-12 · current release · diff ↗
archivedRemoved from CRAN
2026-06-11
issues were not corrected in time
2.0.4
record
2026-06-04 · diff ↗
2.0.3
record
2026-05-13 · diff ↗
2.0.2
record
2026-04-25 · diff ↗ ·
removed 2 exports
HarmonyMatrix, moe_ridge_get_betas
R
R 4.6.0 released · 2026-04-24
1.2.4
record
2025-10-10 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.3
record
2024-11-28 · diff ↗
1.2.1
record
2024-08-28 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
record
2023-11-29 · diff ↗
1.1.0
record
2023-10-23 · diff ↗
1.0.3
record
2023-10-01 · diff ↗
1.0.1
record
2023-09-20 · diff ↗ ·
added 1 export
harmony_options

Show 7 earlier eventsHide 7 earlier events

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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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