Files in connorhknight/IBRAP_no_decontX

Integrated Benchmarking scRNA-seq Analytical Pipeline

R/IBRAP-object.R R/Read10X_output.R R/add.cell.cycle.R R/add.feature.score.R R/aslist.R R/benchmark.clustering.R R/benchmark.intergation.R R/bracketsubset.R R/bracketsubset_replace.R R/cell_metadata.R R/colnames.R R/convert_subset_index.R R/createIBRAPobject.R R/dim.R R/dollarsubset.R R/feature_metadata.R R/filter_IBRAP.R R/find_neighbours.R R/find_percentage_genes.R R/isUnique.R R/merge.R R/methods-object.R R/ncol_methods_method.R R/nrow_methods_method.R R/perform.GO.enrichment.R R/perform.bbknn.R R/perform.diffusion.map.R R/perform.harmony.R R/perform.lvish.R R/perform.pca.R R/perform.reduction.kmeans.R R/perform.sc3.reduction.cluster.R R/perform.sc3.slot.cluster.R R/perform.scanorama.R R/perform.scanpy.normalisation.R R/perform.scran.normalisation.R R/perform.scrublet.R R/perform.sct.normalisation.R R/perform.seurat.cluster.R R/perform.seurat.diffexp.R R/perform.seurat.diffexp.all.R R/perform.seurat.subclustering.R R/perform.singleR.annotation.R R/perform.slingshot.trajectory.R R/perform.tpm.normalisation.R R/perform.tsne.R R/perform.umap.R R/plot.GO.output.R R/plot.QC.scatter.R R/plot.QC.vln.R R/plot.cluster.benchmarking.R R/plot.dot.plot.R R/plot.features.R R/plot.integration.benchmarking.R R/plot.reduced.dim.R R/plot.reduced.dim.interactive.R R/plot.slingshot.R R/plot.vln.R R/prepare.reticulate.R R/remove.hvgs.R R/rownames.R R/run.IBRAP.rshiny.R R/seurat_integration.R R/show.R R/singelbracketsubset.R inst/rshiny/app.R man/IBRAP-object.Rd man/Read10X_output.Rd man/add.cell.cycle.Rd man/add.feature.score.Rd man/as_list_methods.Rd man/benchmark.clustering.Rd man/benchmark.integration.Rd man/cell_metadata.Rd man/createIBRAPobject.Rd man/dim.Rd man/dollar.Rd man/feature_metadata.Rd man/filter_IBRAP.Rd man/find_percentage_genes.Rd man/isUnique.Rd man/merge.Rd man/methods-object.Rd man/ncol.Rd man/nrow.Rd man/perform.GO.enrichment.Rd man/perform.bbknn.Rd man/perform.diffexp.Rd man/perform.diffexp.all.Rd man/perform.diffusion.map.Rd man/perform.graph.cluster.Rd man/perform.graph.subclustering.Rd man/perform.harmony.Rd man/perform.lvish.Rd man/perform.nn.Rd man/perform.pca.Rd man/perform.reduction.kmeans.Rd man/perform.sc3.reduction.cluster.Rd man/perform.sc3.slot.cluster.Rd man/perform.scanorama.Rd man/perform.scanpy.Rd man/perform.scran.Rd man/perform.scrublet.Rd man/perform.sct.Rd man/perform.seurat.cca.Rd man/perform.singleR.annotation.Rd man/perform.slingshot.trajectory.Rd man/perform.tpm.Rd man/perform.tsne.Rd man/perform.umap.Rd man/plot.GO.output.Rd man/plot.QC.scatter.Rd man/plot.QC.vln.Rd man/plot.dot.plot.Rd man/plot.features.Rd man/plot.reduced.dim.Rd man/plot.reduced.dim.interactive.Rd man/plot.slingshot.Rd man/plot.vln.Rd man/prepare.reticulate.Rd man/remove.hvgs.Rd man/rownames.Rd man/run.IBRAP.rshiny.Rd man/sub-IBRAP-ANY-ANY-ANY-method.Rd