Package: harmony
Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
Version: 2.0.4
Authors@R: c(
    person("Nikolaos", "Patikas", email = "nik.patik@gmail.com",
        role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-3978-0134")),
    person("Hongcheng", "Yao", email = "hongchengyaonk@gmail.com",
        role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-0743-4835")),
    person("Ilya", "Korsunsky", email = "ilya.korsunsky@gmail.com",
        role = c("cre", "aut"), comment = c(ORCID = "0000-0003-4848-3948")),
    person("Martin", "Hemberg", email = "mhemberg@bwh.harvard.edu",
        role = c("aut"), comment = c(ORCID = "0000-0001-8895-5239")),   
    person("Nghia", "Millard", email = "nmillard@g.harvard.edu",
        role = "aut", comment = c(ORCID = "0000-0002-0518-7674")),
    person("Jean", "Fan", email = "jeanfan@fas.harvard.edu",
        role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-0212-5451")),
    person("Kamil", "Slowikowski", email = "kslowikowski@gmail.com",
        role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-2843-6370")),
    person("Miles", "Smith",
        role = c("ctb")),
    person("Soumya", "Raychaudhuri",
        role = c("aut"), comment = c(ORCID = "0000-0002-1901-8265"))
    )
Description: 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.
URL: https://github.com/immunogenomics/harmony,
        https://pati-ni.github.io/harmony/
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.3
Depends: R(>= 4.2.0), Rcpp
LazyData: true
LazyDataCompression: gzip
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Imports: dplyr, cowplot, ggplot2, Matrix, methods, tibble, rlang,
        RhpcBLASctl, cli
Suggests: SingleCellExperiment, Seurat (>= 4.1.1), testthat, knitr,
        rmarkdown, ggthemes, ggrepel, patchwork, tidyverse, tidyr,
        data.table
VignetteBuilder: knitr
Repository: https://immunogenomics.r-universe.dev
Date/Publication: 2026-06-05 17:44:33 UTC
RemoteUrl: https://github.com/immunogenomics/harmony
RemoteRef: HEAD
RemoteSha: df19af23ae0639bd6ea2da63898f973f08c85862
NeedsCompilation: yes
Packaged: 2026-06-05 20:23:39 UTC; root
Author: Nikolaos Patikas [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-3978-0134>),
  Hongcheng Yao [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-0743-4835>),
  Ilya Korsunsky [cre, aut] (ORCID:
    <https://orcid.org/0000-0003-4848-3948>),
  Martin Hemberg [aut] (ORCID: <https://orcid.org/0000-0001-8895-5239>),
  Nghia Millard [aut] (ORCID: <https://orcid.org/0000-0002-0518-7674>),
  Jean Fan [aut, ctb] (ORCID: <https://orcid.org/0000-0002-0212-5451>),
  Kamil Slowikowski [aut, ctb] (ORCID:
    <https://orcid.org/0000-0002-2843-6370>),
  Miles Smith [ctb],
  Soumya Raychaudhuri [aut] (ORCID:
    <https://orcid.org/0000-0002-1901-8265>)
Maintainer: Ilya Korsunsky <ilya.korsunsky@gmail.com>