Files in ImmuneDynamics/Spectre
High-dimensional cytometry and imaging analysis.
.Rbuildignore
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
R/BatchAdjust.R
R/FIt-SNE.R
R/create.dt.R
R/create.stats.R
R/create.sumtable.R
R/demo.asinh.R
R/demo.batches.1.R
R/demo.clustered.R
R/demo.exp.R
R/demo.start.R
R/demo.sum.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/make.autograph.R
R/make.colour.plot.R
R/make.multi.plot.R
R/make.network.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.chronoclust.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.prepare.chronoclust.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
R/write.sumtables.R
README.md
data/demo.asinh.RData
data/demo.batches.1.RData
data/demo.clustered.RData
data/demo.exp.RData
data/demo.start.RData
data/demo.sum.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/create.dt.Rd
man/create.stats.Rd
man/create.sumtable.Rd
man/demo.asinh.Rd
man/demo.batches.1.Rd
man/demo.clustered.Rd
man/demo.exp.Rd
man/demo.start.Rd
man/demo.sum.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.embed.columns.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/fftRtsne.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.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.chronoclust.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.prepare.chronoclust.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
man/write.sumtables.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/CNS_Mock_01.fcs
scripts/Plotting cytobank/CNS_Mock_02.fcs
scripts/Plotting cytobank/CNS_Mock_03.fcs
scripts/Plotting cytobank/CNS_WNV_D7_01.fcs
scripts/Plotting cytobank/CNS_WNV_D7_02.fcs
scripts/Plotting cytobank/CNS_WNV_D7_03.fcs
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/filtered_gene_bc_matrices/hg19/barcodes.tsv
scripts/scRNAseq/filtered_gene_bc_matrices/hg19/genes.tsv
scripts/scRNAseq/filtered_gene_bc_matrices/hg19/matrix.mtx
scripts/scRNAseq/scRNAseq.R
tests/function_tests/test_fitsne.R
tests/hex_plots/DimRed_HexPlotdemo.csv
tests/hex_plots/test_script.R
tests/test_fitsne.R
tests/test_logicle.R
tests/test_network_plot.R
workflows/Alignment workflows/Spectre CytoNorm workflow/CytoNorm workflow.R
workflows/Alignment workflows/data/Mock_01_A.csv
workflows/Alignment workflows/data/Mock_02_A.csv
workflows/Alignment workflows/data/Mock_03_A.csv
workflows/Alignment workflows/data/Mock_04_A.csv
workflows/Alignment workflows/data/Mock_05_B.csv
workflows/Alignment workflows/data/Mock_06_B.csv
workflows/Alignment workflows/data/Mock_07_B.csv
workflows/Alignment workflows/data/Mock_08_B.csv
workflows/Alignment workflows/data/Virus_01_A.csv
workflows/Alignment workflows/data/Virus_02_A.csv
workflows/Alignment workflows/data/Virus_03_A.csv
workflows/Alignment workflows/data/Virus_04_A.csv
workflows/Alignment workflows/data/Virus_05_B.csv
workflows/Alignment workflows/data/Virus_06_B.csv
workflows/Alignment workflows/data/Virus_07_B.csv
workflows/Alignment workflows/data/Virus_08_B.csv
workflows/Alignment workflows/metadata/sample.details.csv
workflows/Classic workflows/Spectre - simple discovery/Spectre simple discovery workflow.R
workflows/Classic workflows/Spectre general discovery workflow/1 - data prep.R
workflows/Classic workflows/Spectre general discovery workflow/2 - batch alignment.R
workflows/Classic workflows/Spectre general discovery workflow/3 - clustering.R
workflows/Classic workflows/Spectre general discovery workflow/4 - quantitative analysis.R
workflows/Classic workflows/data/CNS_Mock_01.csv
workflows/Classic workflows/data/CNS_Mock_02.csv
workflows/Classic workflows/data/CNS_Mock_03.csv
workflows/Classic workflows/data/CNS_Mock_04.csv
workflows/Classic workflows/data/CNS_Mock_05.csv
workflows/Classic workflows/data/CNS_Mock_06.csv
workflows/Classic workflows/data/CNS_WNV_D7_01.csv
workflows/Classic workflows/data/CNS_WNV_D7_02.csv
workflows/Classic workflows/data/CNS_WNV_D7_03.csv
workflows/Classic workflows/data/CNS_WNV_D7_04.csv
workflows/Classic workflows/data/CNS_WNV_D7_05.csv
workflows/Classic workflows/data/CNS_WNV_D7_06.csv
workflows/Classic workflows/metadata/sample.details.csv
workflows/Classification_workflow/Classification_workflow.Rmd
workflows/Classification_workflow/Classification_workflow.html
workflows/Spatial - FlowJo/Spectre TIFF to FCS/TIFF to FCS.R
workflows/Spatial - FlowJo/data/ROIs/ROI002/CD11b_Sm149.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/CD20_Dy161.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/CD3_Er170.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/CD45_Sm152.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/CD4_Gd156.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/CD8a_Dy162.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/DNA1_Ir191.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI002/DNA3_Ir193.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/CD11b_Sm149.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/CD20_Dy161.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/CD3_Er170.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/CD45_Sm152.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/CD4_Gd156.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/CD8a_Dy162.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/DNA1_Ir191.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI004/DNA3_Ir193.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/CD11b_Sm149.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/CD20_Dy161.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/CD3_Er170.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/CD45_Sm152.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/CD4_Gd156.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/CD8a_Dy162.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/DNA1_Ir191.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI006/DNA3_Ir193.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/CD11b_Sm149.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/CD20_Dy161.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/CD3_Er170.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/CD45_Sm152.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/CD4_Gd156.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/CD8a_Dy162.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/DNA1_Ir191.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI008/DNA3_Ir193.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/CD11b_Sm149.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/CD20_Dy161.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/CD3_Er170.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/CD45_Sm152.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/CD4_Gd156.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/CD8a_Dy162.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/DNA1_Ir191.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI010/DNA3_Ir193.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/CD11b_Sm149.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/CD20_Dy161.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/CD3_Er170.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/CD45_Sm152.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/CD4_Gd156.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/CD8a_Dy162.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/DNA1_Ir191.tiff
workflows/Spatial - FlowJo/data/ROIs/ROI012/DNA3_Ir193.tiff
workflows/Spatial - FlowJo/data/masks/ROI002_ilastik_s2_Object Identities.tif
workflows/Spatial - FlowJo/data/masks/ROI002_ilastik_s2_Object Predictions.tif
workflows/Spatial - FlowJo/data/masks/ROI002_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - FlowJo/data/masks/ROI004_ilastik_s2_Object Identities.tif
workflows/Spatial - FlowJo/data/masks/ROI004_ilastik_s2_Object Predictions.tif
workflows/Spatial - FlowJo/data/masks/ROI004_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - FlowJo/data/masks/ROI006_ilastik_s2_Object Identities.tif
workflows/Spatial - FlowJo/data/masks/ROI006_ilastik_s2_Object Predictions.tif
workflows/Spatial - FlowJo/data/masks/ROI006_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - FlowJo/data/masks/ROI008_ilastik_s2_Object Identities.tif
workflows/Spatial - FlowJo/data/masks/ROI008_ilastik_s2_Object Predictions.tif
workflows/Spatial - FlowJo/data/masks/ROI008_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - FlowJo/data/masks/ROI010_ilastik_s2_Object Identities.tif
workflows/Spatial - FlowJo/data/masks/ROI010_ilastik_s2_Object Predictions.tif
workflows/Spatial - FlowJo/data/masks/ROI010_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - FlowJo/data/masks/ROI012_ilastik_s2_Object Identities.tif
workflows/Spatial - FlowJo/data/masks/ROI012_ilastik_s2_Object Predictions.tif
workflows/Spatial - FlowJo/data/masks/ROI012_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - FlowJo/metadata/sample.metadata.csv
workflows/Spatial - advanced/Spectre advanced spatial/Adv spatial 1 - add masks.R
workflows/Spatial - advanced/Spectre advanced spatial/Adv spatial 2 - cellular analysis.R
workflows/Spatial - advanced/Spectre advanced spatial/Adv spatial 3 - quantitative analysis.R
workflows/Spatial - advanced/data/ROIs/ROI002/CD11b_Sm149.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/CD20_Dy161.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/CD3_Er170.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/CD45_Sm152.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/CD4_Gd156.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/CD8a_Dy162.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/DNA1_Ir191.tiff
workflows/Spatial - advanced/data/ROIs/ROI002/DNA3_Ir193.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/CD11b_Sm149.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/CD20_Dy161.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/CD3_Er170.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/CD45_Sm152.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/CD4_Gd156.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/CD8a_Dy162.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/DNA1_Ir191.tiff
workflows/Spatial - advanced/data/ROIs/ROI004/DNA3_Ir193.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/CD11b_Sm149.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/CD20_Dy161.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/CD3_Er170.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/CD45_Sm152.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/CD4_Gd156.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/CD8a_Dy162.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/DNA1_Ir191.tiff
workflows/Spatial - advanced/data/ROIs/ROI006/DNA3_Ir193.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/CD11b_Sm149.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/CD20_Dy161.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/CD3_Er170.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/CD45_Sm152.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/CD4_Gd156.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/CD8a_Dy162.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/DNA1_Ir191.tiff
workflows/Spatial - advanced/data/ROIs/ROI008/DNA3_Ir193.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/CD11b_Sm149.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/CD20_Dy161.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/CD3_Er170.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/CD45_Sm152.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/CD4_Gd156.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/CD8a_Dy162.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/DNA1_Ir191.tiff
workflows/Spatial - advanced/data/ROIs/ROI010/DNA3_Ir193.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/CD11b_Sm149.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/CD20_Dy161.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/CD3_Er170.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/CD45_Sm152.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/CD4_Gd156.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/CD8a_Dy162.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/DNA1_Ir191.tiff
workflows/Spatial - advanced/data/ROIs/ROI012/DNA3_Ir193.tiff
workflows/Spatial - advanced/data/Segmentation - process TIFFs.R
workflows/Spatial - advanced/data/masks/ROI002_ilastik_s2_Object Identities.tif
workflows/Spatial - advanced/data/masks/ROI002_ilastik_s2_Object Predictions.tif
workflows/Spatial - advanced/data/masks/ROI002_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - advanced/data/masks/ROI004_ilastik_s2_Object Identities.tif
workflows/Spatial - advanced/data/masks/ROI004_ilastik_s2_Object Predictions.tif
workflows/Spatial - advanced/data/masks/ROI004_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - advanced/data/masks/ROI006_ilastik_s2_Object Identities.tif
workflows/Spatial - advanced/data/masks/ROI006_ilastik_s2_Object Predictions.tif
workflows/Spatial - advanced/data/masks/ROI006_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - advanced/data/masks/ROI008_ilastik_s2_Object Identities.tif
workflows/Spatial - advanced/data/masks/ROI008_ilastik_s2_Object Predictions.tif
workflows/Spatial - advanced/data/masks/ROI008_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - advanced/data/masks/ROI010_ilastik_s2_Object Identities.tif
workflows/Spatial - advanced/data/masks/ROI010_ilastik_s2_Object Predictions.tif
workflows/Spatial - advanced/data/masks/ROI010_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - advanced/data/masks/ROI012_ilastik_s2_Object Identities.tif
workflows/Spatial - advanced/data/masks/ROI012_ilastik_s2_Object Predictions.tif
workflows/Spatial - advanced/data/masks/ROI012_ilastik_s2_Simple Segmentation.tif
workflows/Spatial - advanced/data/multicut_1_pixel.ilp
workflows/Spatial - advanced/data/multicut_2_segment.ilp
workflows/Spatial - advanced/data/multicut_3_cellClassification.ilp
workflows/Spatial - advanced/data/multicut_4_regionClassification.ilp
workflows/Spatial - advanced/metadata/sample.metadata.csv
workflows/Spatial - simple/Spectre simple spatial/Simple spatial 1 - add masks.R
workflows/Spatial - simple/Spectre simple spatial/Simple spatial 2 - cellular analysis.R
workflows/Spatial - simple/Spectre simple spatial/Simple spatial 3 - quantitative analysis.R
workflows/Spatial - simple/data/BasicSegmentation_MAC.cpproj
workflows/Spatial - simple/data/BasicSegmentation_WINDOWS.cpproj
workflows/Spatial - simple/data/ROIs/ROI002/CD11b_Sm149.tiff
workflows/Spatial - simple/data/ROIs/ROI002/CD20_Dy161.tiff
workflows/Spatial - simple/data/ROIs/ROI002/CD3_Er170.tiff
workflows/Spatial - simple/data/ROIs/ROI002/CD45_Sm152.tiff
workflows/Spatial - simple/data/ROIs/ROI002/CD4_Gd156.tiff
workflows/Spatial - simple/data/ROIs/ROI002/CD8a_Dy162.tiff
workflows/Spatial - simple/data/ROIs/ROI002/DNA1_Ir191.tiff
workflows/Spatial - simple/data/ROIs/ROI002/DNA3_Ir193.tiff
workflows/Spatial - simple/data/ROIs/ROI004/CD11b_Sm149.tiff
workflows/Spatial - simple/data/ROIs/ROI004/CD20_Dy161.tiff
workflows/Spatial - simple/data/ROIs/ROI004/CD3_Er170.tiff
workflows/Spatial - simple/data/ROIs/ROI004/CD45_Sm152.tiff
workflows/Spatial - simple/data/ROIs/ROI004/CD4_Gd156.tiff
workflows/Spatial - simple/data/ROIs/ROI004/CD8a_Dy162.tiff
workflows/Spatial - simple/data/ROIs/ROI004/DNA1_Ir191.tiff
workflows/Spatial - simple/data/ROIs/ROI004/DNA3_Ir193.tiff
workflows/Spatial - simple/data/ROIs/ROI006/CD11b_Sm149.tiff
workflows/Spatial - simple/data/ROIs/ROI006/CD20_Dy161.tiff
workflows/Spatial - simple/data/ROIs/ROI006/CD3_Er170.tiff
workflows/Spatial - simple/data/ROIs/ROI006/CD45_Sm152.tiff
workflows/Spatial - simple/data/ROIs/ROI006/CD4_Gd156.tiff
workflows/Spatial - simple/data/ROIs/ROI006/CD8a_Dy162.tiff
workflows/Spatial - simple/data/ROIs/ROI006/DNA1_Ir191.tiff
workflows/Spatial - simple/data/ROIs/ROI006/DNA3_Ir193.tiff
workflows/Spatial - simple/data/ROIs/ROI008/CD11b_Sm149.tiff
workflows/Spatial - simple/data/ROIs/ROI008/CD20_Dy161.tiff
workflows/Spatial - simple/data/ROIs/ROI008/CD3_Er170.tiff
workflows/Spatial - simple/data/ROIs/ROI008/CD45_Sm152.tiff
workflows/Spatial - simple/data/ROIs/ROI008/CD4_Gd156.tiff
workflows/Spatial - simple/data/ROIs/ROI008/CD8a_Dy162.tiff
workflows/Spatial - simple/data/ROIs/ROI008/DNA1_Ir191.tiff
workflows/Spatial - simple/data/ROIs/ROI008/DNA3_Ir193.tiff
workflows/Spatial - simple/data/ROIs/ROI010/CD11b_Sm149.tiff
workflows/Spatial - simple/data/ROIs/ROI010/CD20_Dy161.tiff
workflows/Spatial - simple/data/ROIs/ROI010/CD3_Er170.tiff
workflows/Spatial - simple/data/ROIs/ROI010/CD45_Sm152.tiff
workflows/Spatial - simple/data/ROIs/ROI010/CD4_Gd156.tiff
workflows/Spatial - simple/data/ROIs/ROI010/CD8a_Dy162.tiff
workflows/Spatial - simple/data/ROIs/ROI010/DNA1_Ir191.tiff
workflows/Spatial - simple/data/ROIs/ROI010/DNA3_Ir193.tiff
workflows/Spatial - simple/data/ROIs/ROI012/CD11b_Sm149.tiff
workflows/Spatial - simple/data/ROIs/ROI012/CD20_Dy161.tiff
workflows/Spatial - simple/data/ROIs/ROI012/CD3_Er170.tiff
workflows/Spatial - simple/data/ROIs/ROI012/CD45_Sm152.tiff
workflows/Spatial - simple/data/ROIs/ROI012/CD4_Gd156.tiff
workflows/Spatial - simple/data/ROIs/ROI012/CD8a_Dy162.tiff
workflows/Spatial - simple/data/ROIs/ROI012/DNA1_Ir191.tiff
workflows/Spatial - simple/data/ROIs/ROI012/DNA3_Ir193.tiff
workflows/Spatial - simple/data/masks/ROI002_Cell_mask.tiff
workflows/Spatial - simple/data/masks/ROI002_Cytoplasm_mask.tiff
workflows/Spatial - simple/data/masks/ROI002_Nuclei_mask.tiff
workflows/Spatial - simple/data/masks/ROI004_Cell_mask.tiff
workflows/Spatial - simple/data/masks/ROI004_Cytoplasm_mask.tiff
workflows/Spatial - simple/data/masks/ROI004_Nuclei_mask.tiff
workflows/Spatial - simple/data/masks/ROI006_Cell_mask.tiff
workflows/Spatial - simple/data/masks/ROI006_Cytoplasm_mask.tiff
workflows/Spatial - simple/data/masks/ROI006_Nuclei_mask.tiff
workflows/Spatial - simple/data/masks/ROI008_Cell_mask.tiff
workflows/Spatial - simple/data/masks/ROI008_Cytoplasm_mask.tiff
workflows/Spatial - simple/data/masks/ROI008_Nuclei_mask.tiff
workflows/Spatial - simple/data/masks/ROI010_Cell_mask.tiff
workflows/Spatial - simple/data/masks/ROI010_Cytoplasm_mask.tiff
workflows/Spatial - simple/data/masks/ROI010_Nuclei_mask.tiff
workflows/Spatial - simple/data/masks/ROI012_Cell_mask.tiff
workflows/Spatial - simple/data/masks/ROI012_Cytoplasm_mask.tiff
workflows/Spatial - simple/data/masks/ROI012_Nuclei_mask.tiff
workflows/Spatial - simple/metadata/ROIs and samples.csv
workflows/Timeseries workflows/Spectre timeseries/Timeseries_workflow.R
workflows/Timeseries workflows/data/BM_Mock 1 CD45+_B cells SCA1+.csv
workflows/Timeseries workflows/data/BM_Mock 1 CD45+_B cells SCA1-.csv
workflows/Timeseries workflows/data/BM_Mock 1 CD45+_Mature Ly6C+ monocyte SCA1+.csv
workflows/Timeseries workflows/data/BM_Mock 1 CD45+_Mature Ly6C- monocyte SCA1-.csv
workflows/Timeseries workflows/data/BM_Mock 1 CD45+_Monoblast SCA1+.csv
workflows/Timeseries workflows/data/BM_Mock 1 CD45+_Monoblast SCA1-.csv
workflows/Timeseries workflows/data/BM_WNV D1 1 CD45+_B cells SCA1+.csv
workflows/Timeseries workflows/data/BM_WNV D1 1 CD45+_B cells SCA1-.csv
workflows/Timeseries workflows/data/BM_WNV D1 1 CD45+_Mature Ly6C+ monocyte SCA1+.csv
workflows/Timeseries workflows/data/BM_WNV D1 1 CD45+_Mature Ly6C- monocyte SCA1-.csv
workflows/Timeseries workflows/data/BM_WNV D1 1 CD45+_Monoblast SCA1+.csv
workflows/Timeseries workflows/data/BM_WNV D1 1 CD45+_Monoblast SCA1-.csv
workflows/Timeseries workflows/data/BM_WNV D2 1 CD45+_B cells SCA1+.csv
workflows/Timeseries workflows/data/BM_WNV D2 1 CD45+_B cells SCA1-.csv
workflows/Timeseries workflows/data/BM_WNV D2 1 CD45+_Mature Ly6C+ monocyte SCA1+.csv
workflows/Timeseries workflows/data/BM_WNV D2 1 CD45+_Mature Ly6C- monocyte SCA1-.csv
workflows/Timeseries workflows/data/BM_WNV D2 1 CD45+_Monoblast SCA1+.csv
workflows/Timeseries workflows/data/BM_WNV D2 1 CD45+_Monoblast SCA1-.csv
workflows/Timeseries workflows/metadata/sample.details.csv
