Skip to content

Lite version of the tool to analyze and visualize CyTOF data (still under development)

Notifications You must be signed in to change notification settings

AlexanderKononov/cytofBrowserLite

Repository files navigation

picture

cytofBrowserLite

The cytofBrowserLite is a lite version of cytofBrowser with reduced number of dependences. This version will be maintained and upgraded..

cytofBrowser

The package focuses on analysis of CyTOF proteomic data by the easiest and fastest way. CytofBrowser allows you to starts from FCS files that you get from the CyTOF machine, preprocessing and transforms the data then getting the specific cell populations by markers as well as by clustering cells, estimate the abundance of cell populations, find the correlations and patterns by high-throughput hypothesis testing algorithm. CytofBrowser supplies the tool to visualize explore and interact with data on each step of the pipeline. picture

Graphical interface

CytofBrowser has a user-friendly graphical interface. It developed as R Shiny app GUI.

Installation

Presently you can install the develop version of this program:

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

Run the cytofBrowser

It assumed that this program will be used with GUI as Shiny App.

cytofBrowser::cytofBrowserGUI()

Troubleshooting

If you can’t install the app correctly: Check the dependencies of packages. List of demanded packages is waited in file DESCRIPTION. Also the same list of the packages mentioned in additional file Library_louncher.R This files can be used as a script to upload all dependencies in the running R session manually.

If you faced with a problem of updating any package from dependencies: Check the R version and Rstudio version (if you use it). After R 4.0 update some packages can not update correctly by the previous R version and can show “non-zero checksum” error. Some basic packages can have problem with updating within Rstudio and show the error “can’t remove the previous version of package”. The most straightforward way to fix this problem is to delete the target package manually from the directory with R package libraries (for windows usually Documents/R/win-library) and there instal it again.

If no one button does not react or collapses the app: One previous version of shinyFiles for windows is not stable. You can try to manually update this package.

install.packages("shinyFiles")

or you can try to use the previous version of the package.

lin <- "https://cran.r-project.org/src/contrib/Archive/shinyFiles/shinyFiles_0.7.5.tar.gz"
install.packages(lin, repos=NULL, type="source")

Since I have not devoted time to create detail documentation yet, I note the link to the video which I sent to my colleague and mentor to get the feedback. It can look redundantly detail or in an odd format. But there are enough explanations of work and examples of a graphical interface using. P.S. Don’t judge my video skills strictly=)

https://youtu.be/rWSD7y0Gaic

About

Lite version of the tool to analyze and visualize CyTOF data (still under development)

Topics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages