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: 1.2.3
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: 2024-11-27
DOI: 10.32614/CRAN.package.harmony
Author: Ilya Korsunsky ORCID iD [cre, aut] (<https://orcid.org/0000-0003-4848-3948>), Martin Hemberg ORCID iD [aut] (<https://orcid.org/0000-0001-8895-5239>), Nikolaos Patikas ORCID iD [aut, ctb] (<https://orcid.org/0000-0002-3978-0134>), Hongcheng Yao ORCID iD [aut, ctb] (<https://orcid.org/0000-0002-0743-4835>), Nghia Millard ORCID iD [aut] (<https://orcid.org/0000-0002-0518-7674>), Jean Fan ORCID iD [aut, ctb] (<https://orcid.org/0000-0002-0212-5451>), Kamil Slowikowski ORCID iD [aut, ctb] (<https://orcid.org/0000-0002-2843-6370>), Miles Smith [ctb], Soumya Raychaudhuri ORCID iD [aut] (<https://orcid.org/0000-0002-1901-8265>)
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_1.2.3.tar.gz
Windows binaries: r-devel: harmony_1.2.3.zip, r-release: harmony_1.2.3.zip, r-oldrel: harmony_1.2.3.zip
macOS binaries: r-release (arm64): harmony_1.2.3.tgz, r-oldrel (arm64): harmony_1.2.3.tgz, r-release (x86_64): harmony_1.2.3.tgz, r-oldrel (x86_64): harmony_1.2.3.tgz
Old sources: harmony archive

Reverse dependencies:

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

Linking:

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