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: 1.2.0
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: 2023-11-29
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: software.broadinstitute.org/harmony
NeedsCompilation: yes
Materials: NEWS
CRAN checks: harmony results

Documentation:

Reference manual: harmony.pdf
Vignettes: Using harmony in Seurat
Detailed Walkthrough of Harmony Algorithm
Quick start to Harmony

Downloads:

Package source: harmony_1.2.0.tar.gz
Windows binaries: r-devel: harmony_1.2.0.zip, r-release: harmony_1.2.0.zip, r-oldrel: harmony_1.2.0.zip
macOS binaries: r-release (arm64): harmony_1.2.0.tgz, r-oldrel (arm64): harmony_1.2.0.tgz, r-release (x86_64): harmony_1.2.0.tgz
Old sources: harmony archive

Reverse dependencies:

Reverse imports: lemur, ProFAST, RaceID, symphony
Reverse suggests: Platypus, Seurat, singleCellTK

Linking:

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