Machine learning & computational biology for cell and gene therapy
Neuroscientist by training. Currently working on machine learning, bioinformatics and statistical analysis in biopharma.
Eight months into vibe coding
Since last winter, I started using Claude Code, then Codex, for my work — my current setup is a Claude Max 5x + ChatGPT Pro. They quickly became something I reach for every day. Below are a couple of notes on customizations I’ve picked up along the way. The first two are for VS Code — I know the CLI is where the bleeding edge lives and is the best supported, but for the analysis work I do I prefer being able to quickly interact with files and plots (usually on a remote EC2 instance). ...
Very basic use of tidyverse in R packages
tl;dr Why bother? .data Alternatives and problems !! + sym filter_ tl;dr 90% of my usecases when putting a function that uses tidyverse with non-standard evaluation (NSE) into an R package can be resolved by importFrom rlang .data. In these cases, I’m only looking for a way to be able to use tidyverse internally in the package, and have it pass the R package check, rather than allowing the user to supply function arguments in the NSE form. ...
Reading Prism files into R
Example Prism files Main functionality Additional features Back in the early days of grad school I used to use Prism GraphPad a lot before switching to R. Prism is a great piece of software and I’ve seen scientists using them a lot. Recently I wanted to import a Prism .pzfx file into R, and as usual, I went to Google expecting there’ll be some readxl or readr equivalent for prism. Surprisingly, I didn’t find much more than this SO question. So, how do you import a prism file into R? The easiest way is probably exporting the prism file to a text file then read it into R. But this just doesn’t feel that good, right? So I started looking into the file structure of .pzfx files and tried to parse it by myself. Starting from Prism5, in addition to the binary file it also stores the data table in XML format which is possible to parse. After some trials and errors I made a little R package (github, CRAN) to read .pzfx files into R data frames. I’ll briefly document how it works here. ...
Show me what you got
The data Make some plots Side Notes Alright, let’s see what we can do here. Too much iris could be boring, so I thought I’d contribute some data by myself. Since my fitbit stopped working early this year, I’ve switched back to my old Garmin forerunner 10, and it turns out that you can downlowd .csv file of previous activities through Garmin connect. Now that’s pretty cool - I’ll just use this data. ...
Hello World
Hello world! This is the end of 2017, and I’m on my winter break. So I thought I’d play with the blogdown package and see if I can come up with some sort of site from within R. So here I am. 你好，世界