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R applications and code snippets useful in my research and possibly for other users as well.

Pophelper

(R Package)

pophelper-githubpophelper is a software tool to aid in the analysis of output files generated from population analysis programs STRUCTURE and TESS. pophelper was developed in R statistical programming language. The pophelper package can be used to tabulate runs, summarise runs, estimate K using the Evanno method, export files for CLUMPP, generate barplot figures etc.

The current version is available at GitHub. More details on installation and usage are provided at the link. For a detailed demonstration, refer this vignette.


Pophelper Structure

(R Shiny Web Application)

pophelper-structure

Pophelper Structure is the online web app version of the `R` package pophelper with some minor changes. `Pophelper Structure` does not require any coding and all interaction happens through a graphical user interface. Pophelper Structure was also developed in `R` and uses `R` shiny and `R` shiny server web framework. Pophelper Structure has been stripped down to the essentials. Alignment using CLUMPP is performed on the fly and results are shown instantly. Users are not required to handle any CLUMPP files.

The webpage can be accessed here at pophelper.com.


Pophelper PCA

(R Shiny Web Application)

Pophelper PCA is an online web app to perform a Principal Component Analysis (PCA) and analyse the results using a scatterplot. The app works with diploid genetic marker data in GeneClass format and haploid genetic data as text format. It has been extended to incorporate non-genetic data in text format. Smaller data can also be copy-pasted into the input editor.

Pophelper PCA will soon be available here.


Time Series Plotter

(R Markdown Shiny Web Application)

timeseries-plotter

The time series web app was designed to read data exported from weighing scales used to monitor honey bee hive in the field and plot results interactively as a time series plot. This app was developed for a particular application and therefore requires specific input type. Here is a sample file if you wish to try the application.

The time series app will be available here.

 

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