cytofkit: cytofkit: an integrated mass cytometry data analysis pipeline

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