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README.md

Histopathology Research Template 🔬

🔬👀📑🗃📊🏨🗄📇📖📝🎶📈📉📃🖍 🔬🔬🏋🚴🚙👨💻 📸📺🎛🔭🔬💊🔐🍫🌸


https://sbalci.github.io/histopathology-template/


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DOI

https://doi.org/10.5281/zenodo.3635430

https://osf.io/3tjfk/

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. lifecycle

Download histopathR Download histopathR Download histopathR Say Thanks! Launch Rstudio Binder

https://github.com/sbalci/histopathology-template

This repository is a template for the codes I use in my and my friends’ histopathology research.


See examples

devtools::install_github("sbalci/histopathR")
rmarkdown::draft(file = "myfile",
                 template = "clinicopathological",
                 package = "histopathR",
                 create_dir = TRUE,
                 edit = TRUE)

How to use

  • In RStudio:

    • Fork this repository. Then use this repository as template as described here.

    • Use RStudio project as described here.

    • Do not forget to change chunk functions to eval = TRUE.

    • This template contains packages using renv.

  • Via Docker:

https://hub.docker.com/r/serdarbalci/clinicopathological

docker pull serdarbalci/clinicopathological

https://twitter.com/serdarbalci/status/1197849208302252032

  • As a standalone app (for mac only):

https://sourceforge.net/projects/histopathr/

https://twitter.com/serdarbalci/status/1198348640294711296

https://serdarbalci.gitbook.io/parapathology/computers/computers#deploying-a-shiny-app-as-a-desktop-application-with-electron

  • As a Shiny app:

Launch here: https://serdarbalci.shinyapps.io/histopathR/

Run in your own computer R session:

library(shiny)
runUrl("https://github.com/sbalci/histopathRshiny/raw/master/histopathRshiny.tar.gz")

Code here: https://github.com/sbalci/histopathRshiny

  • As a jamovi module:

Download module here:

https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/ClinicoPath.jmo

https://github.com/sbalci/ClinicoPathJamoviModule

https://sourceforge.net/projects/clinicopathjamovimodule/


Recommended Links for Reproducible Research

Please Give Me FeedBack

https://goo.gl/forms/YjGZ5DHgtPlR1RnB3


🔬🔬🔬🔬🔬

UNDER CONSTRUCTION 🛠⛔️⚠️🔩

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A work by Serdar Balci

drserdarbalci@gmail.com