DESCRIPTION

Package: IP4CI
Type: Package
Title: IP4CI: an interpretable pathway-based computational method for cross-species cell-type identification from single cell data
Version: 0.1.0
Author: Rawan Olayan
Maintainer: The package maintainer <rawanolayan@fas.harvard.edu>
Description: More about what it does (maybe more than one line)
    Use four spaces when indenting paragraphs within the Description.
License: What license is it under?
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Collate: 
    'run_packages.R'
    'RnamingCTconv.R'
    'calcLogFC.R'
    'calcSim_avgCT.R'
    'createDir.R'
    'run_09_detectUnknownCT.R'
    'df2obj.R'
    'getCommonGenesPerPathway.R'
    'getCommonPathways.R'
    'getEnrichedGenes.R'
    'getMetadataStat.R'
    'getOverlapMarkers.R'
    'getPathwaysInfo.R'
    'jaccard.R'
    'mergeMultiFiles.R'
    'performMarkersAnalysis.R'
    'plotMetadataStat.R'
    'plotRankingG.R'
    'plotRankingP.R'
    'processCCAres_allCT.R'
    'processCCAres_perCT.R'
    'processObj.R'
    'rankPathwaysCorrelation.R'
    'rankPathwaysRegression.R'
    'runGSEA.R'
    'run_00_preprocessData.R'
    'run_01_processData.R'
    'run_02_gsea.R'
    'run_02_gseaFast.R'
    'run_03_sampleScoring.R'
    'run_04_mergeTwoDatasets.R'
    'run_05_CCA.R'
    'run_06_similarityCalculation.R'
    'run_07_rankPathways.R'
    'run_08_rankGenes.R'
    'visData.R'
    'visObj.R'
    'getVariableFeatures.R'
    'plotCombineRankingPathways.R'
    'checkGexprDensity.R'
    'processIntegratedres_allCT.R'
    'run_05_dataIntegration.R'
    'run_06_similarityCalculationIntegration.R'
    'runIP4CI.R'
    'runIP4CI_ct.R'
    'SubsetObjVarF.R'
  'selectCCA.R'
Suggests: 
    knitr,
    rmarkdown
VignetteBuilder: knitr
Imports: 
    olsrr,
    BiocParallel,
    devtools,
    gridExtra,
    matrixStats,
    STRINGdb,
    corpcor,
    mixOmics,
    reticulate,
    ggplot2,
    ggpubr,
    RColorBrewer,
    psych,
    reshape,
    Seurat,
    ggrepel,
    fastICA,
    pheatmap,
    corrplot,
    rbioapi,
    PRROC,
    ReactomePA,
    uwot,
    plyr,
    org.Mm.eg.db,
    org.Hs.eg.db,
    reactome.db,
    clusterProfiler,
    sjmisc,
    stringr,
    dplyr,
    irlba,
    ComplexHeatmap