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Detail analysis and visualisation CyTOF data
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README.md

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cytofCore

Travis build status AppVeyor build status Codecov test coverage

Description: The package focuses on analysis of CyTOF proteomic data. It is of the pipeline which starts from fcs files and goes to markers and cell type abundance correlation analysis through marker filtratio and cell clusterisation steps. Despite that, there are functions available for interactive R session, it is assumed that cytofCore are run with a graphical interface as R Shiny app GUI.

Installation

Presently you can instal the develop version of this programme:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
    
devtools::install_github("AlexanderKononov/cytofCore")

On the current stage of the project develop there are few dependency packages which don't instal and deploy automatically, such as (flowCore, FlowSOM, ConsensusClusterPlus). I advise to instal they manually:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    
BiocManager::install("flowCore")
BiocManager::install("FlowSOM")
BiocManager::install("ConsensusClusterPlus")

Complete list of dependencies is listed in the DESCRIPTION and in the file Library_louncher.R

In a future, you can install the released version of cytofCore from Bioconductor with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cytofCore")

Run the cytofCore

I assumed that this programme will be used with GUI as Shiny App.

cytofCoreGUI()

Example

This is a basic example which shows you how to run the cytofCore:

library(cytofCore)
#> Warning: replacing previous import 'dplyr::filter' by 'flowCore::filter' when
#> loading 'cytofCore'
#> Warning: replacing previous import 'dplyr::count' by 'matrixStats::count' when
#> loading 'cytofCore'
cytofCoreGUI()
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