Files in ImmuneDynamics/Spectre
High-dimensional cytometry and imaging analysis
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
R/BatchAdjust.R
R/FIt-SNE.R
R/adjust.files.R
R/check.files.R
R/create.dt.R
R/create.stats.R
R/create.sumtable.R
R/demo.clustered.R
R/do.add.cols.R
R/do.add.masks.R
R/do.add.percell.R
R/do.aggregate.R
R/do.align.R
R/do.asinh.R
R/do.calculate.area.R
R/do.clip.R
R/do.combine.cols.R
R/do.create.outlines.R
R/do.extract.R
R/do.extract.cell.dat.R
R/do.filter.R
R/do.filter.percell.R
R/do.label.from.polygon.R
R/do.list.summary.R
R/do.list.switch.R
R/do.logicle.R
R/do.merge.files.R
R/do.pull.data.R
R/do.reorder.R
R/do.rescale.R
R/do.stats.R
R/do.subsample.R
R/do.zscore.R
R/fast.colour.plot.R
R/fast.multi.plot.R
R/make.autograph.R
R/make.colour.plot.R
R/make.multi.plot.R
R/make.pheatmap.R
R/make.spatial.plot.R
R/make.volcano.plot.R
R/package.check.R
R/package.install.R
R/package.load.R
R/prep.cytonorm.R
R/read.files.R
R/read.spatial.files.R
R/run.align.R
R/run.cytonorm.R
R/run.fitsne.R
R/run.flowsom.R
R/run.harmony.R
R/run.knn.classifier.R
R/run.pca.R
R/run.phenograph.R
R/run.rpca.R
R/run.ruv.R
R/run.spatial.analysis.R
R/run.tsne.R
R/run.umap.R
R/spatial.object.R
R/train.cytonorm.R
R/train.knn.classifier.R
R/write.files.R
R/write.hdf5.R
README.md
data/demo.clustered.RData
docker/Dockerfile
image/Spectre.png
image/image
inst/FItSNE_executable/FItSNE-Windows-1.2.1/FItSNE.exe
inst/FItSNE_executable/FItSNE-Windows-1.2.1/libfftw3-3.dll
inst/FItSNE_executable/FItSNE_Unix_1_2_1
man/adjust.files.Rd
man/check.files.Rd
man/create.dt.Rd
man/create.stats.Rd
man/create.sumtable.Rd
man/demo.clustered.Rd
man/do.add.cols.Rd
man/do.add.masks.Rd
man/do.add.percell.Rd
man/do.aggregate.Rd
man/do.align.Rd
man/do.asinh.Rd
man/do.calculate.area.Rd
man/do.clip.Rd
man/do.combine.cols.Rd
man/do.create.outlines.Rd
man/do.extract.Rd
man/do.extract.cell.dat.Rd
man/do.filter.Rd
man/do.filter.percell.Rd
man/do.label.from.polygon.Rd
man/do.list.summary.Rd
man/do.list.switch.Rd
man/do.logicle.Rd
man/do.merge.files.Rd
man/do.pull.data.Rd
man/do.reorder.Rd
man/do.rescale.Rd
man/do.stats.Rd
man/do.subsample.Rd
man/do.zscore.Rd
man/fast.colour.plot.Rd
man/fast.multi.plot.Rd
man/fftRtsne.Rd
man/make.autograph.Rd
man/make.colour.plot.Rd
man/make.multi.plot.Rd
man/make.pheatmap.Rd
man/make.spatial.plot.Rd
man/make.volcano.plot.Rd
man/package.check.Rd
man/package.install.Rd
man/package.load.Rd
man/prep.cytonorm.Rd
man/read.files.Rd
man/read.spatial.files.Rd
man/run.align.Rd
man/run.cytonorm.Rd
man/run.fitsne.Rd
man/run.flowsom.Rd
man/run.harmony.Rd
man/run.knn.classifier.Rd
man/run.pca.Rd
man/run.phenograph.Rd
man/run.rpca.Rd
man/run.ruv.Rd
man/run.spatial.analysis.Rd
man/run.tsne.Rd
man/run.umap.Rd
man/spatial-class.Rd
man/train.cytonorm.Rd
man/train.knn.classifier.Rd
man/write.files.Rd
man/write.hdf5.Rd
other/Modified bodenmiller/1_panel/panel.csv
other/Modified bodenmiller/1_panel/panel_template.csv
other/Modified bodenmiller/2_jupyter/segmentation_script.ipynb
other/Modified bodenmiller/3_cell_class/1_prepare_ilastik.cpproj
scripts/Classifier/Classifier_workflow.R
scripts/Classifier/Classifier_workflow_2.R
scripts/Classifier/run.classifier.R
scripts/ColumnNames/ColumnNames.R
scripts/File table/FileTable.R
scripts/Plotting cytobank/Plotting.R
scripts/Split FCS files/Split FCS files.R
scripts/Stats/Spectre stats.R
scripts/Stats/sum.dat.csv
scripts/scRNAseq/scRNAseq.R
workflows/CellProfiler segmentation/BasicSegmentation_MAC.cpproj
workflows/CellProfiler segmentation/BasicSegmentation_WINDOWS.cpproj
workflows/Ilastik multicut/Segmentation - process TIFFs.R
workflows/Ilastik multicut/multicut_1_pixel.ilp
workflows/Ilastik multicut/multicut_2_segment.ilp
workflows/Ilastik multicut/multicut_3_cellClassification.ilp
workflows/Ilastik multicut/multicut_4_regionClassification.ilp
workflows/Spectre CytoNorm/CytoNorm workflow.R
workflows/Spectre chronoclust/ChronoClust.R
workflows/Spectre kNN classification/Classification_workflow.Rmd
workflows/Spectre kNN classification/Classification_workflow.html
workflows/Spectre rPCA/Spectre rPCA.R
workflows/Spectre simple discovery/Spectre simple discovery workflow.R
workflows/Spectre spatial (FlowJo)/TIFF to FCS.R
workflows/Spectre spatial (advanced)/Adv spatial 1 - add masks.R
workflows/Spectre spatial (advanced)/Adv spatial 2 - cellular analysis.R
workflows/Spectre spatial (advanced)/Adv spatial 3 - quantitative analysis.R
workflows/Spectre spatial (simple)/Simple spatial 1 - add masks.R
workflows/Spectre spatial (simple)/Simple spatial 2 - cellular analysis.R
workflows/Spectre spatial (simple)/Simple spatial 3 - quantitative analysis.R
