Files in zh542370159/SCP
Single Cell Pipeline
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/RcppExports.R
R/SCP-analysis.R
R/SCP-app.R
R/SCP-cell_annotation.R
R/SCP-cellqc.R
R/SCP-feature_annotation.R
R/SCP-imputation.R
R/SCP-plot.R
R/SCP-projection.R
R/SCP-workflow.R
R/Seurat-function.R
R/data.R
R/ggsankey.R
R/reexports.R
R/utils.R
R/zzz.R
README.Rmd
README.md
SCP.Rproj
_pkgdown.yml
data/ifnb_sub.rda
data/lifemap_cell.rda
data/lifemap_compartment.rda
data/lifemap_organ.rda
data/palette_list.rda
data/panc8_sub.rda
data/pancreas_sub.rda
data/ref_scHCL.rda
data/ref_scMCA.rda
data/ref_scZCL.rda
data/words_excluded.rda
inst/python/SCP_analysis.py
inst/python/__pycache__/SCP_analysis.cpython-36.pyc
inst/python/__pycache__/SCP_analysis.cpython-37.pyc
inst/python/__pycache__/SCP_analysis.cpython-38.pyc
inst/python/harmonizomeapi.py
man/AnnotateFeatures.Rd
man/BBKNN_integrate.Rd
man/CC_GenePrefetch.Rd
man/CSS_integrate.Rd
man/CellCorHeatmap.Rd
man/CellDensityPlot.Rd
man/CellDimPlot.Rd
man/CellDimPlot3D.Rd
man/CellScoring.Rd
man/CellStatPlot.Rd
man/ComBat_integrate.Rd
man/Conos_integrate.Rd
man/CreateDataFile.Rd
man/CreateMetaFile.Rd
man/DefaultReduction.Rd
man/DynamicHeatmap.Rd
man/DynamicPlot.Rd
man/EnrichmentPlot.Rd
man/Env_requirements.Rd
man/FeatureCorPlot.Rd
man/FeatureDimPlot.Rd
man/FeatureDimPlot3D.Rd
man/FeatureHeatmap.Rd
man/FeatureStatPlot.Rd
man/FetchH5.Rd
man/GSEAPlot.Rd
man/GeneConvert.Rd
man/GraphPlot.Rd
man/GroupHeatmap.Rd
man/Harmony_integrate.Rd
man/Integration_SCP.Rd
man/LIGER_integrate.Rd
man/LineagePlot.Rd
man/ListDB.Rd
man/MNN_integrate.Rd
man/PAGAPlot.Rd
man/PrepareDB.Rd
man/PrepareEnv.Rd
man/PrepareSCExplorer.Rd
man/ProjectionPlot.Rd
man/RecoverCounts.Rd
man/RenameClusters.Rd
man/RenameFeatures.Rd
man/RunCSSMap.Rd
man/RunCellQC.Rd
man/RunDEtest.Rd
man/RunDM.Rd
man/RunDimReduction.Rd
man/RunDoubletCalling.Rd
man/RunDynamicEnrichment.Rd
man/RunDynamicFeatures.Rd
man/RunEnrichment.Rd
man/RunFR.Rd
man/RunGLMPCA.Rd
man/RunGSEA.Rd
man/RunHarmony2.Rd
man/RunKNNMap.Rd
man/RunKNNPredict.Rd
man/RunLargeVis.Rd
man/RunMDS.Rd
man/RunMonocle2.Rd
man/RunMonocle3.Rd
man/RunNMF.Rd
man/RunPAGA.Rd
man/RunPCAMap.Rd
man/RunPHATE.Rd
man/RunPaCMAP.Rd
man/RunPalantir.Rd
man/RunSCExplorer.Rd
man/RunSCVELO.Rd
man/RunScmap.Rd
man/RunSeuratMap.Rd
man/RunSingleR.Rd
man/RunSlingshot.Rd
man/RunSymphonyMap.Rd
man/RunTriMap.Rd
man/RunUMAP2.Rd
man/RunWOT.Rd
man/Scanorama_integrate.Rd
man/Seurat_integrate.Rd
man/SrtAppend.Rd
man/SrtReorder.Rd
man/Standard_SCP.Rd
man/StatPlot.Rd
man/Uncorrected_integrate.Rd
man/VelocityPlot.Rd
man/VolcanoPlot.Rd
man/adata_to_srt.Rd
man/adjcolors.Rd
man/as_matrix.Rd
man/blendcolors.Rd
man/capitalize.Rd
man/check_DataType.Rd
man/check_Python.Rd
man/check_R.Rd
man/check_srtList.Rd
man/check_srtMerge.Rd
man/compute_velocity_on_grid.Rd
man/conda_install.Rd
man/conda_python.Rd
man/db_DoubletDetection.Rd
man/db_Scrublet.Rd
man/db_scDblFinder.Rd
man/db_scds.Rd
man/download.Rd
man/drop_data.Rd
man/env_exist.Rd
man/exist_Python_pkgs.Rd
man/fastMNN_integrate.Rd
man/figures/CellDimPlot3D-1.png
man/figures/DynamicHeatmap-1.png
man/figures/DynamicPlot-1.png
man/figures/EDA-1.png
man/figures/EDA-2.png
man/figures/EDA-3.png
man/figures/EDA-4.png
man/figures/EDA-5.png
man/figures/Enrichment_comparison-1.png
man/figures/Enrichment_enrichmap-1.png
man/figures/Example-1.jpg
man/figures/Example-2.jpg
man/figures/Example-3.jpg
man/figures/Example-4.jpg
man/figures/FeatureDimPlot3D-1.png
man/figures/FeatureHeatmap-1.png
man/figures/FeatureStatPlot-1.png
man/figures/GSEA_bar-1.png
man/figures/GSEA_comparison-1.png
man/figures/Integration-all.png
man/figures/Integration_SCP-1.png
man/figures/RunCellQC-1.png
man/figures/RunCellQC-2.png
man/figures/RunCellQC-3.png
man/figures/RunDEtest-1.png
man/figures/RunEnrichment-1.png
man/figures/RunEnrichment-2.png
man/figures/RunEnrichment-3.png
man/figures/RunEnrichment-4.png
man/figures/RunGSEA-1.png
man/figures/RunKNNMap-1.png
man/figures/RunKNNPredict-bulk-1.png
man/figures/RunKNNPredict-scrna-1.png
man/figures/RunKNNPredict-scrna-2.png
man/figures/RunKNNPredict-scrna-3.png
man/figures/RunPAGA-1.png
man/figures/RunSCVELO-1.png
man/figures/RunSCVELO-2.png
man/figures/RunSlingshot-1.png
man/figures/RunSlingshot-2.png
man/figures/RunSlingshot-3.png
man/figures/SCExplorer-1.png
man/figures/SCExplorer-2.png
man/figures/Standard_SCP-1.png
man/find_conda.Rd
man/geom_alluvial.Rd
man/geom_alluvial_label.Rd
man/geom_sankey.Rd
man/geom_sankey_bump.Rd
man/geom_sankey_label.Rd
man/get_vars.Rd
man/ifnb_sub.Rd
man/installed_Python_pkgs.Rd
man/invoke.Rd
man/isOutlier.Rd
man/iterchunks.Rd
man/lifemap_cell.Rd
man/make_long.Rd
man/palette_list.Rd
man/palette_scp.Rd
man/panc8_sub.Rd
man/pancreas_sub.Rd
man/panel_fix.Rd
man/reexports.Rd
man/ref_scHCL.Rd
man/scVI_integrate.Rd
man/segementsDf.Rd
man/show_palettes.Rd
man/slim_data.Rd
man/srt_to_adata.Rd
man/theme_blank.Rd
man/theme_sankey.Rd
man/theme_scp.Rd
man/tochunks.Rd
man/try_get.Rd
man/unnest.Rd
man/words_excluded.Rd
src/RcppExports.cpp
src/asMatrix.cpp
