DESCRIPTION

Package: RIRA
Type: Package
Title: A package for the Rhesus Immune Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells
Version: 1.0.0
Author: Bimber Lab
Description: Wrappers and pipelines to process single-cell RNA-seq data for RIRA
Encoding: UTF-8
URL: https://bimberlab.github.io/RIRA/
LazyData: true
Maintainer: Bimber Lab <bimber@ohsu.edu>
License: GPL-3
Depends:
    R (>= 4.3.0),
Imports:
    Seurat,
    SeuratObject,
    rlang,
    scGate,
    UCell (>= 2.6.0),
    dplyr,
    Matrix,
    SingleCellExperiment,
    ExperimentHub,
    DropletUtils,
    utils,
    cFIT,
    DALEX,
    DALEXtra,
    mlr3verse,
    mlr3learners,
    mlr3tuning,
    mlr3,
    ranger,
    knitr,
    caret,
    future,
    methods,
    stats,
    ggplot2,
    egg,
    reticulate,
    naturalsort,
    patchwork,
    BiocParallel,
    ggcorrplot,
    magrittr,
    mlr3verse,
    httr
Suggests:
    devtools,
    testthat (>= 2.1.0),
    SeuratData,
    rmdformats,
    RCurl
Remotes:
    pengminshi/cFIT,
    SeuratData=bbimber/seurat-data,
    carmonalab/UCell,
    carmonalab/scGate
RoxygenNote: 7.3.2
Collate: 
    'Utils.R'
    'CellTypist.R'
    'Classification.R'
    'ComponentScores.R'
    'Phenotyping.R'
    'GeneModules.R'
    'cFIT.R'
    'scGate.R'
VignetteBuilder: knitr