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cytofkit (version 1.4.4)

cytofkit: an integrated mass cytometry data analysis pipeline

Description

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

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Version

Version

1.4.4

License

Artistic-2.0

Maintainer

Jinmiao Chen

Last Published

February 15th, 2017

Functions in cytofkit (1.4.4)

detect_anoms_sd

Outlier detection
applyComp

apply compensation on the FCS expression data
DensVM

Density-based local maxima cluster with SVM
scaleData

rescale the data
cytof_dimReduction

Dimension reduction for high dimensional data
clusterAssign

assign clusters to non-peak points
cytof_progression

Progression estimation of cytof expression data
find_neighbors

K Nearest Neighbour Search
Rphenograph

RphenoGraph clustering
cytof_exprsMerge

Merge the expression matrix from multiple FCS files with preprocessing
cytof_clusterPlot

Scatter plot of the cluster results
ClusterX

Fast clustering by automaticly search and find of density peaks
autoLgcl

a modified version of "estimateLogicle" from flowCore
cytof_addToFCS

Add data to the original FCS files
launchShinyAPP_GUI

GUI for launching shiny APP
localDensity

Computes the local density of points in a data matrix
cytofAsinh

Noise reduced arsinh transformation
minDistToHigher

Calculate distance to nearest observation of higher density
FlowSOM_integrate2cytofkit

FlowSOM algorithm
cytofkit-package

cytofkit: an integrated mass cytometry data analysis pipeline
cytofkitNews

check the package update news
cytof_heatmap

Heatmap plot of cluster mean value results
peakDetect

Automatic peak detection
cytof_writeResults

Save the cytofkit analysis results
getParameters_GUI

GUI for marker selection
cytofkit

cytofkit: an integrated mass cytometry data analysis pipeline
cytof_progressionPlot

Progression plot
cytof_exprsExtract

Extract the expression data from a FCS file with preprocessing
cytofkitShinyAPP

A Shiny app to interactively visualize the analysis results
estimateDc

Estimate the distance cutoff (density neighbourhood) from down-sampled data
cytof_cluster

Subset detection by clustering
haloDetect

differentiate halo form cores
peaksGamma_plot

Plot varaition of peak nums with increasing gamma
cytofkit_GUI

The user friendly GUI client for cytofkit-package