Files in sydneycytometry/Spectre
A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data.
.Rbuildignore
.gitignore
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.aggregate.R
R/do.align.R
R/do.asinh.R
R/do.clip.R
R/do.filter.R
R/do.list.summary.R
R/do.list.switch.R
R/do.logicle.R
R/do.merge.files.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.volcano.plot.R
R/package.check.R
R/package.install.R
R/package.load.R
R/prep.cytonorm.R
R/read.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.ruv.R
R/run.tsne.R
R/run.umap.R
R/train.cytonorm.R
R/train.knn.classifier.R
R/write.files.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.aggregate.Rd
man/do.align.Rd
man/do.asinh.Rd
man/do.clip.Rd
man/do.embed.columns.Rd
man/do.filter.Rd
man/do.list.summary.Rd
man/do.list.switch.Rd
man/do.logicle.Rd
man/do.merge.files.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.volcano.plot.Rd
man/package.check.Rd
man/package.install.Rd
man/package.load.Rd
man/prep.cytonorm.Rd
man/read.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.ruv.Rd
man/run.tsne.Rd
man/run.umap.Rd
man/train.cytonorm.Rd
man/train.knn.classifier.Rd
man/write.files.Rd
man/write.sumtables.Rd
scripts/Classifier/Classifier_workflow.R
scripts/Classifier/Classifier_workflow_2.R
scripts/Classifier/run.classifier.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/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
worked_examples/General_discovery_workflow/Spectre 1 - discovery prep.R
worked_examples/General_discovery_workflow/Spectre 2 - batch alignment.R
worked_examples/General_discovery_workflow/Spectre 3 - discovery clustering.R
worked_examples/General_discovery_workflow/Spectre 4 - discovery quantitative analysis.R
worked_examples/General_discovery_workflow/data/Mock_01_A.csv
worked_examples/General_discovery_workflow/data/Mock_02_A.csv
worked_examples/General_discovery_workflow/data/Mock_03_A.csv
worked_examples/General_discovery_workflow/data/Mock_04_A.csv
worked_examples/General_discovery_workflow/data/Mock_05_B.csv
worked_examples/General_discovery_workflow/data/Mock_06_B.csv
worked_examples/General_discovery_workflow/data/Mock_07_B.csv
worked_examples/General_discovery_workflow/data/Mock_08_B.csv
worked_examples/General_discovery_workflow/data/Virus_01_A.csv
worked_examples/General_discovery_workflow/data/Virus_02_A.csv
worked_examples/General_discovery_workflow/data/Virus_03_A.csv
worked_examples/General_discovery_workflow/data/Virus_04_A.csv
worked_examples/General_discovery_workflow/data/Virus_05_B.csv
worked_examples/General_discovery_workflow/data/Virus_06_B.csv
worked_examples/General_discovery_workflow/data/Virus_07_B.csv
worked_examples/General_discovery_workflow/data/Virus_08_B.csv
worked_examples/General_discovery_workflow/metadata/sample.details.csv
worked_examples/Simple_discovery_workflow/Spectre simple discovery workflow.R
worked_examples/Simple_discovery_workflow/data/CNS_Mock_01.csv
worked_examples/Simple_discovery_workflow/data/CNS_Mock_02.csv
worked_examples/Simple_discovery_workflow/data/CNS_Mock_03.csv
worked_examples/Simple_discovery_workflow/data/CNS_Mock_04.csv
worked_examples/Simple_discovery_workflow/data/CNS_Mock_05.csv
worked_examples/Simple_discovery_workflow/data/CNS_Mock_06.csv
worked_examples/Simple_discovery_workflow/data/CNS_WNV_D7_01.csv
worked_examples/Simple_discovery_workflow/data/CNS_WNV_D7_02.csv
worked_examples/Simple_discovery_workflow/data/CNS_WNV_D7_03.csv
worked_examples/Simple_discovery_workflow/data/CNS_WNV_D7_04.csv
worked_examples/Simple_discovery_workflow/data/CNS_WNV_D7_05.csv
worked_examples/Simple_discovery_workflow/data/CNS_WNV_D7_06.csv
worked_examples/Simple_discovery_workflow/metadata/sample.details.csv
worked_examples/Timeseries_workflow/Timeseries_workflow.R
worked_examples/Timeseries_workflow/data/BM_Mock 1 CD45+_B cells SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_Mock 1 CD45+_B cells SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_Mock 1 CD45+_Mature Ly6C+ monocyte SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_Mock 1 CD45+_Mature Ly6C- monocyte SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_Mock 1 CD45+_Monoblast SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_Mock 1 CD45+_Monoblast SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_WNV D1 1 CD45+_B cells SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_WNV D1 1 CD45+_B cells SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_WNV D1 1 CD45+_Mature Ly6C+ monocyte SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_WNV D1 1 CD45+_Mature Ly6C- monocyte SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_WNV D1 1 CD45+_Monoblast SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_WNV D1 1 CD45+_Monoblast SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_WNV D2 1 CD45+_B cells SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_WNV D2 1 CD45+_B cells SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_WNV D2 1 CD45+_Mature Ly6C+ monocyte SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_WNV D2 1 CD45+_Mature Ly6C- monocyte SCA1-.csv
worked_examples/Timeseries_workflow/data/BM_WNV D2 1 CD45+_Monoblast SCA1+.csv
worked_examples/Timeseries_workflow/data/BM_WNV D2 1 CD45+_Monoblast SCA1-.csv
worked_examples/Timeseries_workflow/metadata/sample.details.csv
