Package: harmony
Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
biocViews: BatchEffect, GeneExpression, RNASeq, SingleCell, Transcriptomics
Version: 1.0
Authors@R: c(
    person("Ilya", "Korsunsky", email = "ilya.korsunsky@gmail.com", 
        role = c("cre", "aut"), comment = c(ORCID = "0000-0003-4848-3948")),
    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 Korsunsky et al <doi.org/10.1101/461954>. Package includes a standalone Harmony function and interfaces to external frameworks.
URL: software.broadinstitute.org/harmony
License: GPL-3 + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.0.2
Depends: R(>= 3.4.0), Rcpp
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
Imports:
    dplyr, 
    cowplot,
    tidyr,
    ggplot2, 
    irlba,
    Matrix,
    methods,
    tibble,
    rlang,
    SingleCellExperiment
Suggests:
    Seurat,
    testthat,
    knitr,
    rmarkdown,
    BiocStyle
VignetteBuilder: knitr