/R-scripting-samples

Example code supporting immunology research

Primary LanguageHTML

Instructions:

[1 of 4] Coding Sample_1 - Automated ELISA data processing

#### PURPOSE OF THE SHINY APPLICATION:

     Example of Shiny app automating research (ELISA) data munging ( non-proprietary source data ).

     Purpose: This app automates processing of common immunology research data (ELISA reader output),

     making such processing faster & less error prone. Cleaned data can be downloaded in 

     'tidy' format, i.e. suitable for Tableau or SQL database. Data are also plotted for 

     quick review and QC of the data. 


#### HOW DO I USE THIS APP?:

     Step 1) Download all files (click the green "Code" button above; download .zip folder)

     Step 2) Extract the zip folder contents 

     Step 3) Open R Studio and run install.packages("shiny") in the console

     Step 4) Open the Shiny app. 

     Step 5) Use the app to upload the example ELISA data, and review the output plots. 

     Step 6) Download the cleaned data for experiment-tailored processing/plotting in Tableau/Spotfire.

[2 of 4] Coding Sample_2 - FACS Analysis & Discussion

#### PURPOSE OF THE CODE:

     Example of R analysis using FACS data ( non-proprietary source data ), 

     including munging, plotting, and analysis narrative.


#### INSTRUCTIONS FOR USE:

     Step 1) Download all files (click the green "Code" button above; download .zip folder)

     Step 2) Extract the zip folder contents

     Step 3) Run the .Rmd file

     Step 4) Use the "Preview" button in R Studio to view the html report output

[3 of 4] Coding Sample_3 - Derivation of a prognostic signature KIRC

#### PURPOSE OF THE CODE:

     This script derives a prognostic signature for renal cell carcinoma using transcriptomic data (from GDC/TCGA)

     Analysis provides an example of of data exploration, differential expression analysis (Voom/Limma),

     and survival analysis ( taken from the GDC public database )


#### How can I run and/or view the analysis?:

     Step 1) Download all files (click the green "Code" button above; download .zip folder)

     Step 2) Extract the zip folder contents

     Step 3) Run the .Rmd file using 'knit' OR just look at the .html file to view analysis.

[4 of 4] Coding Sample_4 - FASTER FACS - Automated processing of FlowJo statistics

#### PURPOSE OF THE SHINY APP:

     Speed up your flow cytometry analysis with the FASTER FACS Shiny App. 

     FASTER FACS lets you upload your raw data & download processed data ready for 

     GraphpadPrism, Tableau, or other BI software.  

     This app automates appx. Twenty-five data processing steps. 


#### HOW DO I USE THIS APP?:

     Step 1) Download app (click the green "Code" button above; download .zip folder)

     Step 2) Extract the zip folder contents

     Step 3) Install both R & R Studio

     Step 4) Open R Studio and run install.packages("shiny") in the console (this only needs to be done once)

     Step 5) Open the "app_FASTER FACS.R" file in R Studio & then click the "Run App" button. 

             The first time the app is run, it will automatically install required R packages. 

             Package installation may take a few minutes, but it will only happen once. Follow the instructions in the app.