histopathology-template

Histopathology Research Template 🔬

🔬👀📑🗃📊🏨🗄📇📖⚗📝🎶📈📉📃🖍 🔬🔬🏋🚴🚙👨💻 📸📺🎛🔭🔬💊🔐🍫🌸

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

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

https://osf.io/3tjfk/

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

See some of the codes here: https://sbalci.github.io/histopathology-template/Report.html
You may also install histopathR package to get all the codes as R Markdown Template.

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

I have tried to collect common codes in My R Codes For Data Analysis. I plan to collect them under the package histopathR gradually.

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

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UNDER CONSTRUCTION 🛠⛔️⚠️🔩

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A work by Serdar Balci

<drserdarbalci@gmail.com>

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