cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline

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An integrated mass cytometry data analysis pipeline that enables simultaneous illustration of cellular diversity and progression.

Author
Jinmiao Chen, Hao Chen
Date of publication
None
Maintainer
Jinmiao Chen <Chen_Jinmiao@immunol.a-star.edu.sg>, Hao Chen <chen_hao@immunol.a-star.edu.sg>
License
Artistic-2.0
Version
1.6.1

View on Bioconductor

Man pages

ClusterX
Fast clustering by automatic search and find of density peaks
cytof_addToFCS
Add data to the original FCS files
cytof_cluster
Subset detection by clustering
cytof_clusterPlot
Scatter plot of the cluster results
cytof_clusterStat
Statistics of the cluster relusts
cytof_colorPlot
Plot the data with color-coded marker values
cytof_dimReduction
Dimension reduction for high dimensional data
cytof_exprsExtract
Extract the expression data from a FCS file with...
cytof_exprsMerge
Merge the expression matrix from multiple FCS files with...
cytof_heatmap
Heatmap plot of cluster mean value results
cytofkit
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkit_GUI
The user friendly GUI client for 'cytofkit-package'
cytofkitNews
check the package update news
cytofkit-package
cytofkit: an integrated mass cytometry data analysis pipeline
cytofkitShinyAPP
A Shiny app to interactively visualize the analysis results
cytof_progression
Progression estimation of cytof expression data
cytof_progressionPlot
Progression plot
cytof_writeResults
Save the cytofkit analysis results
DensVM
Density-based local maxima cluster with SVM
getParameters_GUI
GUI for marker selection
launchShinyAPP_GUI
GUI for launching shiny APP
Rphenograph
RphenoGraph clustering

Files in this package

cytofkit/DESCRIPTION
cytofkit/NAMESPACE
cytofkit/R
cytofkit/R/ClusterX.R
cytofkit/R/DensVM.R
cytofkit/R/RcppExports.R
cytofkit/R/Rphenograph.R
cytofkit/R/cytof_cluster.R
cytofkit/R/cytof_dimensionReduction.R
cytofkit/R/cytof_postProcess.R
cytofkit/R/cytof_preProcess.R
cytofkit/R/cytof_progression.R
cytofkit/R/cytofkit.R
cytofkit/R/cytofkit_GUI.R
cytofkit/Rplots.pdf
cytofkit/build
cytofkit/build/vignette.rds
cytofkit/inst
cytofkit/inst/CITATION
cytofkit/inst/NEWS.Rd
cytofkit/inst/doc
cytofkit/inst/doc/cytofkit_example.R
cytofkit/inst/doc/cytofkit_example.Rmd
cytofkit/inst/doc/cytofkit_example.html
cytofkit/inst/doc/cytofkit_shinyAPP.R
cytofkit/inst/doc/cytofkit_shinyAPP.Rmd
cytofkit/inst/doc/cytofkit_shinyAPP.html
cytofkit/inst/doc/cytofkit_workflow.R
cytofkit/inst/doc/cytofkit_workflow.Rmd
cytofkit/inst/doc/cytofkit_workflow.html
cytofkit/inst/extdata
cytofkit/inst/extdata/130515_C2_stim_CD19-.fcs
cytofkit/inst/extdata/demo_fcs.RData
cytofkit/inst/extdata/help.gif
cytofkit/inst/extdata/help.png
cytofkit/inst/extdata/parameter.txt
cytofkit/inst/shiny
cytofkit/inst/shiny/global.R
cytofkit/inst/shiny/server.R
cytofkit/inst/shiny/ui.R
cytofkit/inst/unitTests
cytofkit/inst/unitTests/test_cytof_dimReduction.R
cytofkit/man
cytofkit/man/ClusterX.Rd
cytofkit/man/DensVM.Rd
cytofkit/man/Rphenograph.Rd
cytofkit/man/cytof_addToFCS.Rd
cytofkit/man/cytof_cluster.Rd
cytofkit/man/cytof_clusterPlot.Rd
cytofkit/man/cytof_clusterStat.Rd
cytofkit/man/cytof_colorPlot.Rd
cytofkit/man/cytof_dimReduction.Rd
cytofkit/man/cytof_exprsExtract.Rd
cytofkit/man/cytof_exprsMerge.Rd
cytofkit/man/cytof_heatmap.Rd
cytofkit/man/cytof_progression.Rd
cytofkit/man/cytof_progressionPlot.Rd
cytofkit/man/cytof_writeResults.Rd
cytofkit/man/cytofkit-package.Rd
cytofkit/man/cytofkit.Rd
cytofkit/man/cytofkitNews.Rd
cytofkit/man/cytofkitShinyAPP.Rd
cytofkit/man/cytofkit_GUI.Rd
cytofkit/man/getParameters_GUI.Rd
cytofkit/man/launchShinyAPP_GUI.Rd
cytofkit/src
cytofkit/src/RcppExports.cpp
cytofkit/src/jaccard_coeff.cpp
cytofkit/tests
cytofkit/tests/runTests.R
cytofkit/vignettes
cytofkit/vignettes/cluster_panel.png
cytofkit/vignettes/cytofkit_GUI.png
cytofkit/vignettes/cytofkit_example.Rmd
cytofkit/vignettes/cytofkit_pipeline.png
cytofkit/vignettes/cytofkit_shinyAPP.Rmd
cytofkit/vignettes/cytofkit_workflow.Rmd
cytofkit/vignettes/load2shiny.png
cytofkit/vignettes/marker_panel.png
cytofkit/vignettes/progression_panel.png
cytofkit/vignettes/sample_panel.png