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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")
AuthorJinmiao Chen, Hao Chen
Bioconductor views BiomedicalInformatics CellBiology Clustering DimensionReduction FlowCytometry GUI
Date of publicationNone
MaintainerJinmiao Chen <Chen_Jinmiao@immunol.a-star.edu.sg>, Hao Chen <chen_hao@immunol.a-star.edu.sg>
LicenseArtistic-2.0
Version1.6.5

View on Bioconductor

Functions

ClusterX Man page
cytof_addToFCS Man page
cytof_cluster Man page
cytof_clusterPlot Man page
cytof_clusterStat Man page
cytof_colorPlot Man page
cytof_dimReduction Man page
cytof_exprsExtract Man page
cytof_exprsMerge Man page
cytof_heatmap Man page
cytofkit Man page
cytofkit_GUI Man page
cytofkitNews Man page
cytofkit-package Man page
cytofkitShinyAPP Man page
cytof_progression Man page
cytof_progressionPlot Man page
cytof_writeResults Man page
DensVM Man page
getParameters_GUI Man page
launchShinyAPP_GUI Man page
Rphenograph Man page
spectral1 Man page
spectral2 Man page

Files

DESCRIPTION
NAMESPACE
R
R/ClusterX.R R/DensVM.R R/RcppExports.R R/Rphenograph.R R/cytof_cluster.R R/cytof_dimensionReduction.R R/cytof_postProcess.R R/cytof_preProcess.R R/cytof_progression.R R/cytofkit.R R/cytofkit_GUI.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/cytofkit_example.R
inst/doc/cytofkit_example.Rmd
inst/doc/cytofkit_example.html
inst/doc/cytofkit_shinyAPP.R
inst/doc/cytofkit_shinyAPP.Rmd
inst/doc/cytofkit_shinyAPP.html
inst/doc/cytofkit_workflow.R
inst/doc/cytofkit_workflow.Rmd
inst/doc/cytofkit_workflow.html
inst/extdata
inst/extdata/130515_C2_stim_CD19-.fcs
inst/extdata/demo_fcs.RData
inst/extdata/help.gif
inst/extdata/help.png
inst/extdata/parameter.txt
inst/shiny
inst/shiny/global.R inst/shiny/server.R inst/shiny/ui.R
inst/unitTests
inst/unitTests/test_cytof_dimReduction.R
man
man/ClusterX.Rd man/DensVM.Rd man/Rphenograph.Rd man/cytof_addToFCS.Rd man/cytof_cluster.Rd man/cytof_clusterPlot.Rd man/cytof_clusterStat.Rd man/cytof_colorPlot.Rd man/cytof_dimReduction.Rd man/cytof_exprsExtract.Rd man/cytof_exprsMerge.Rd man/cytof_heatmap.Rd man/cytof_progression.Rd man/cytof_progressionPlot.Rd man/cytof_writeResults.Rd man/cytofkit-package.Rd man/cytofkit.Rd man/cytofkitNews.Rd man/cytofkitShinyAPP.Rd man/cytofkit_GUI.Rd man/getParameters_GUI.Rd man/launchShinyAPP_GUI.Rd man/spectral1.Rd man/spectral2.Rd
src
src/RcppExports.cpp
src/jaccard_coeff.cpp
tests
tests/runTests.R
vignettes
vignettes/cluster_panel.png
vignettes/cytofkit_GUI.png
vignettes/cytofkit_example.Rmd
vignettes/cytofkit_pipeline.png
vignettes/cytofkit_shinyAPP.Rmd
vignettes/cytofkit_workflow.Rmd
vignettes/load2shiny.png
vignettes/marker_panel.png
vignettes/progression_panel.png
vignettes/sample_panel.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.