BinMat: an R package and app to process fragment analysis data

BinMat: developed by Clarke van Steenderen
BinMat: developed by Clarke van Steenderen

Clarke van Steenderen is a current CBC PhD student, and his research focuses on how genetic variation affects the performance of biological control agents. He has come through the ranks at Rhodes University as an undergraduate BSc student at Rhodes, and has worked on a variety of species, with a particular focus on genetics. His Master’s degree focused on the biological control of Cactaceous weeds in South Africa, with a particular emphasis on the genetic relationships within the Dactylopius genus (the ‘cochineal’ bugs).

Based on his experience with the analysis of genetic data and using R, Clarke has developed a package called ‘BinMat’ (Binary Matrix). This package was accepted into the R CRAN repository in March 2020 – those of you familiar with R will know that this being added to the realm of R packages is not inconsequential! All the functions in the package are also available in the form of a user-friendly application (graphical user interface), created using the R Shiny platform.

Clarke developed the package and app for the processing of binary fragment analysis data such as ISSRs (inter-simple sequence repeats) and AFLPs (amplified fragment length polymorphisms). BinMat consolidates replicate sample pairs in a binary dataset (presence/absence data) into consensus reads, produces summary statistics, and allows the user to visualise their data as ordination plots and clustering trees without having to use multiple software programs and input files, or rely on previous programming experience.

He has made a tutorial video that accompanies this R package – available in the link below. Links to Clarke’s related resources for this BinMat code are available on the CBC Google Site – here.

These additional resources include the R code used in the tutorial, a document that provides links to the R Shiny application, and relevant code housed on GitHub.

YouTube tutorial video for BinMat:
Part 1: https://www.youtube.com/watch?v=RTHf7Naqr10
Part 2: https://www.youtube.com/watch?v=jk4uBzVgqw8

For further information or inquiries, Clarke can be contacted on vsteenderen@gmail.com.

Source:  CBC Staff and Students

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