PCR Calculator
We do a LOT of PCR in the Andersen lab and instead of having to calculate how much “master mix” to make for each different-sized PCR by hand (or using EXCEL), I decided to design a shiny app that could be used on my phone at my bench for extra ease! It is extremely useful for me, probably the most useful thing I have done in graduate school (and it only took ~30 minutes!).
HTA dilutions calculation
I created this shiny application to help members of the lab (including myself) easily and accurately perform drug dilutions for the high-throughput sorter assay. When I first joined the lab, Erik ran a script that performed the necessary calculations for each person before every assay. Over time, it became necessary to calculate my own dilutions. I first created a markdown script that eventually evolved to this user-friendly application.
Fine-map QTL with NIL phenotypes
I wanted to create an application that could be used to easily view and interact with NIL phenotype data generated from the sorter. Every time that I ran an assay I had to look at 5-20 different traits, in both control and drug conditions and drug conditions with and without regression. It soon became an exhausting task. I developed this app to help myself and others analyze NIL data quickly and use the “show QTL?” button to narrow a complex NIL interval.
Andersen Lab Linkage Mapping Analysis
I created this application to help members of the Andersen Lab quickly look at QTL mapping data results. It was important to me that this application not only plotted the data, but also allowed for quick fine-mapping of QTL to identify potential candidate genes that might be causing drug resistance using gene functional descriptions, GO annotations, and overlapping eQTL.
Andersen Lab NIL Genotype Browser
I created this application because I felt that the current NIL browser (here) was not useful for what I needed. This simple application allows users to search for NILs by genomic region or plot specific user-designated strains.