Files in tomashhurst/Spectre

A Toolbox for the Analysis of High-Dimensional Cytometry and Single-Cell Data

R/demo.asinh.R R/demo.clustered.R R/demo.exp.R R/demo.start.R R/demo.sum.R R/do.add.cols.R R/do.aggregate.R R/do.align.R R/do.asinh.R R/do.list.summary.R R/do.list.switch.R R/do.merge.files.R R/do.noise.reduce.R R/do.normalise.R R/do.prep.fsom.R R/do.stats.R R/do.subsample.R R/do.zscore.R R/make.autograph.R R/make.colour.plot.R R/make.multi.plot.R R/make.network.plot.R R/make.pheatmap.R R/make.volcano.plot.R R/package.check.R R/package.install.R R/package.load.R R/read.files.R R/run.chronoclust.R R/run.flowsom.R R/run.knn.classifier.R R/run.pca.R R/run.prepare.chronoclust.R R/run.train.knn.classifier.R R/run.tsne.R R/run.umap.R R/write.files.R R/write.sumtables.R README.md man/demo.asinh.Rd man/demo.clustered.Rd man/demo.exp.Rd man/demo.start.Rd man/demo.sum.Rd man/do.add.cols.Rd man/do.aggregate.Rd man/do.align.Rd man/do.asinh.Rd man/do.embed.columns.Rd man/do.list.summary.Rd man/do.list.switch.Rd man/do.merge.files.Rd man/do.noise.reduce.Rd man/do.normalise.Rd man/do.prep.fsom.Rd man/do.stats.Rd man/do.subsample.Rd man/do.zscore.Rd man/make.autograph.Rd man/make.colour.plot.Rd man/make.multi.plot.Rd man/make.network.plot.Rd man/make.pheatmap.Rd man/make.volcano.plot.Rd man/package.check.Rd man/package.install.Rd man/package.load.Rd man/read.files.Rd man/run.chronoclust.Rd man/run.flowsom.Rd man/run.knn.classifier.Rd man/run.pca.Rd man/run.prepare.chronoclust.Rd man/run.train.knn.classifier.Rd man/run.tsne.Rd man/run.umap.Rd man/write.files.Rd man/write.sumtables.Rd scripts/Batch_alignment/Batch_alignment.R scripts/Classifier/Classifier_workflow.R scripts/Classifier/run.classifier.R scripts/Cluster_annotation/Spectre_cluster_annotation.R scripts/Merged quantification and stats/Spectre - merged quantification and stats.R scripts/Split FCS files/Split FCS files.R scripts/SumTables_Graphing/Spectre_sumtables_graphing.R scripts/Write sumtables/Write sumtables.R scripts/do.train.align.R scripts/make.colour.plot.R scripts/write.double.pos.R tests/hex_plots/test_script.R tests/test.network.plot.R worked_examples/Classifier_workflow/Classifier_workflow.R worked_examples/Simple discovery workflow/Spectre simple discovery workflow.R worked_examples/Spectre_discovery_workflow/Spectre A - discovery prep.R worked_examples/Spectre_discovery_workflow/Spectre B - discovery clustering.R worked_examples/Spectre_discovery_workflow/Spectre C - discovery quantitative analysis.R worked_examples/Timeseries_workflow/Timeseries_workflow.R