README.md

Histopathology Research Template 🔬

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

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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.

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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.

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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/

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Recommended Links for Reproducible Research

• Reproducible Templates for Analysis and Dissemination

• Happy Git and GitHub for the useR

• R-Giris Dersi Sunum

• R-Giris Dersi

• R-Markdown Dersi Sunum

• R-Markdown Dersi

• How to Prepare Data for Histopathology Research pdf

• How to Prepare Data for Histopathology Research

• How to Prepare Data for Histopathology Research Presentation

• “The Quartz guide to bad data”nın Türkçe çevirisi: Kötü Veri Kılavuzu

• Create A MS Word Template for R Markdown

Please Give Me FeedBack

https://goo.gl/forms/YjGZ5DHgtPlR1RnB3

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UNDER CONSTRUCTION 🛠⛔️⚠️🔩

Follow @serdarbalci

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A work by Serdar Balci

[email protected]