AlkaBenawra/MDMAPR: Molecular Detection Mapping and Analysis Platform for R

Runs a Shiny web application that merges raw 'qPCR' fluorescence data with related metadata to visualize species presence/absence detection patterns and assess data quality. The application calculates threshold values from raw fluorescence data using a method based on the second derivative method, Luu-The et al (2005) <doi:10.2144/05382RR05>, and utilizes the ‘chipPCR’ package by Rödiger, Burdukiewicz, & Schierack (2015) <doi:10.1093/bioinformatics/btv205> to calculate Cq values. The application has the ability to connect to a custom developed MySQL database to populate the applications interface. The application allows users to interact with visualizations such as a dynamic map, amplification curves and standard curves, that allow for zooming and/or filtering. It also enables the generation of customized exportable reports based on filtered mapping data.

install.packages("remotes")
remotes::install_github("AlkaBenawra/MDMAPR")