DESCRIPTION

Package: HemaScopeR
Type: Package
Title: HemaScopeR: a user-friendly and modular design R package tailored for analyzing single-cell and spatial transcriptome sequencing data of hematopoietic cells
Version: 1.0.0
Author: Zhenyi Wang <wangzy17@tsinghua.org.cn> and Yuxin Miao <miaoyx21@mails.tsinghua.edu.cn>
Maintainer: Zhenyi Wang <wangzy17@tsinghua.org.cn> and Yuxin Miao <miaoyx21@mails.tsinghua.edu.cn>
Description: HemaScopeR, a specialized bioinformatics toolkit designed for comprehensive analysis of 
             scRNA-seq and st-seq data derived from hematopoietic cells, including those from myeloid and lymphoid lineages.
Depends: R (>= 4.3)
Imports: devtools, Seurat, Rfast2, hdf5r, ggpubr, SeuratWrappers, monocle, slingshot, GSVA, org.Mm.eg.db,
         org.Hs.eg.db, scran, AUCell, RcisTarget, GENIE3, biomaRt, velocyto.R, limma, ComplexHeatmap, scmap, clusterProfiler,
         doMC, doRNG, shinyjs, shiny, shinyWidgets, shinydashboard, slickR, phateR, gelnet, parallelDist, kableExtra,
         transport, feather, markdown, ggalluvial, forcats, mcmc, MCMCpack, fields, CellChat, presto, SCENIC,
         abcCellmap, copykat, DoubletFinder, SeuratDisk
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Collate: 
    'MERFISH_Step1_Loading_Data.R'
    'MERFISH_Step2_QC.R'
    'MERFISH_Step3_Clustering.R'
    'MERFISH_Step5_SpatiallyVariableFeatures.R'
    'MERFISH_Step6_Interaction.R'
    'MERFISH_Step7_CellCycle.R'
    'OpenXGR_oColormap.R'
    'OpenXGR_oDefineNet.R'
    'OpenXGR_oGGnetwork.R'
    'OpenXGR_oIG2TB.R'
    'OpenXGR_oLayout.R'
    'OpenXGR_oNetInduce.R'
    'OpenXGR_oRDS.R'
    'OpenXGR_oSubneterGenes.R'
    'OpenXGR_oTB2IG.R'
    'install_python.R'
    'main_MERFISH_pipeline.R'
    'main_st_10x_visium_pipeline.R'
    'main_stereo_pipeline.R'
    'sc_10x_chromium_mainPipeline.R'
    'sc_Step10_calculate_lineage_scores.R'
    'sc_Step11_run_GSVA.R'
    'sc_Step12_prepareDataForScvelo.R'
    'sc_Step12_run_monocle.R'
    'sc_Step12_run_slingshot.R'
    'sc_Step13_run_SCENIC.R'
    'sc_Step14_run_CellChat.R'
    'sc_Step2_QC_multiple_scRNASeq.R'
    'sc_Step2_QC_single_scRNASeq.R'
    'sc_Step4_CNV_analysis.R'
    'sc_Step4_cellAnnotation.R'
    'sc_Step4_query_data.R'
    'sc_Step5_run_phateR.R'
    'sc_Step7_assign_cell_cycle.R'
    'sc_Step8_heterogeneity.R'
    'sc_Step9_violin_plot_for_marker_genes.R'
    'sc_assistantFunctions.R'
    'sc_doublerFinderwraper.R'
    'st_10x_visium_mainPipeline.R'
    'st_Step10_NicheAnalysis.R'
    'st_Step1_Loading_Data.R'
    'st_Step2_QC_spatial.R'
    'st_Step3_Clustering.R'
    'st_Step4_Find_DEGs.R'
    'st_Step5_SpatiallyVariableFeatures.R'
    'st_Step6_Interaction.R'
    'st_Step7_CNV_analysis.R'
    'st_Step8_Deconvolution.R'
    'st_Step9_Cellcycle.R'
    'st_assistantFunctions.R'
    'stereo_Step1_Loading_Data.R'