Files in bimberlabinternal/RIRA_classification
A package for the Rhesus Immune Reference Atlas (RIRA): A multi-tissue single-cell landscape of immune cells
.Rbuildignore
.dockerignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yml
.gitignore
CITATION.cff
DESCRIPTION
Dockerfile
NAMESPACE
R/CellTypist.R
R/Classification.R
R/ComponentScores.R
R/GeneModules.R
R/Phenotyping.R
R/Utils.R
R/scGate.R
README.md
_pkgdown.yml
inst/components/TCR_EarlyStimulationComponent.tsv
inst/components/TCR_StimulationComponent1.tsv
inst/components/Tcell_EffectorDifferentiation.tsv
inst/components/Tcell_NaiveToEffector.tsv
inst/extdata/humanRibosomalGenes_Human_GRCh38_p13_Ensembl.tsv
inst/extdata/metadata.csv
inst/gates/ActiveAvEp.RM.tsv
inst/gates/AvEp.RM.tsv
inst/gates/Bcell.RM.tsv
inst/gates/Complement.RM.tsv
inst/gates/Epithelial.RM.tsv
inst/gates/Epithelial.tsv
inst/gates/Erythrocyte.RM.tsv
inst/gates/Erythrocyte.tsv
inst/gates/Fibroblast.RM.tsv
inst/gates/Hepatocyte.RM.tsv
inst/gates/Mesothelial.RM.tsv
inst/gates/Myelocytes.RM.tsv
inst/gates/Myeloid.RM.tsv
inst/gates/Myofibroblast.RM.tsv
inst/gates/NK.RM.tsv
inst/gates/NeutrophilLineage.RM.tsv
inst/gates/PlasmaCell.RM.tsv
inst/gates/Platelet.RM.tsv
inst/gates/Platelet_MK.tsv
inst/gates/Stromal.RM.tsv
inst/gates/Stromal.tsv
inst/gates/Tcell.RM.tsv
inst/gates/Tcell.tsv
inst/gates/demo_gate.tsv
inst/gates/master_table.tsv
inst/gates/pDC.RM.tsv
inst/gates/pDC.tsv
inst/models/CD4vCD8vGDvNK.pkl
inst/models/CD4vCD8vGDvNK_v2.pkl
inst/models/RIRA_FineScope_Myeloid_v3.pkl
inst/models/RIRA_Immune_v1.pkl
inst/models/RIRA_Immune_v2.pkl
inst/models/RIRA_TNK_v2.pkl
man/AssignCellType.Rd
man/CalculateUCellScores.Rd
man/Classify_ImmuneCells.Rd
man/Classify_Myeloid.Rd
man/Classify_TNK.Rd
man/DownloadFromGEO.Rd
man/ExpandGeneList.Rd
man/ExtractGeneWeights.Rd
man/FilterDisallowedClasses.Rd
man/GetAvailableScGates.Rd
man/GetGeneSet.Rd
man/GetMMul10IgGenes.Rd
man/GetMMul10TcrGenes.Rd
man/GetScGateModel.Rd
man/GetSeed.Rd
man/InterpretModels.Rd
man/ListGeneSets.Rd
man/MakePhenotypingDotPlot.Rd
man/PlotImmuneMarkers.Rd
man/PlotMarkerSeries.Rd
man/PlotUcellCorrelation.Rd
man/PredictCellTypeProbability.Rd
man/RunCellTypist.Rd
man/RunScGate.Rd
man/RunScGateForModels.Rd
man/RunScGateWithDefaultModels.Rd
man/RunScGateWithRhesusModels.Rd
man/ScoreCellsWithSavedModel.Rd
man/ScoreUsingSavedComponent.Rd
man/SetSeed.Rd
man/TrainCellTypist.Rd
man/TrainModel.Rd
man/TrainModelsFromSeurat.Rd
tests/testthat.R
tests/testthat/installSeuratData.R
tests/testthat/test-celltypist.R
tests/testthat/test-classification.R
tests/testthat/test-geo.R
tests/testthat/test-phenotyping.R
tests/testthat/test-scgate.R
vignettes/.gitignore
vignettes/CellType.Rmd
vignettes/GetRira.Rmd
vignettes/TCellDifferentiation.Rmd
vignettes/img/GZM_Plot.png
vignettes/img/RIRA_UMAP.png
vignettes/img/RIRA_UMAP_Myeloid.png
vignettes/img/RIRA_UMAP_TNK.png
vignettes/img/TCellSubtype.png
vignettes/img/TCell_EDS.png
