Struggling through scons
I think scons is pretty much dying as a workflow manager, but unfortunately I have to make updates to a pipeline based on it still. Eventually the goal is to...
Recent Posts
Future on R
I recently learned that my simple parallelization code relying on the future and future.lapply packages in RStudio on OpenOnDemand in a Singularity image on ...
Integrating spatial datasets with SCTransform and feature selection
I’ve started working on a few different spatial datasets, as we have our workflow set up around Seurat (you can view our Docker images for our analyses) that...
What’s new January and a bit of February 2025
I didn’t make this a 2025 resolution or anything, but after writing the quick SRA post last month and reviving my site I realized it doesn’t take all that mu...
More up-to-date notes on using Aspera command line to upload to NCBI
I recently had to go through the very frustrating process of uploading fastqs to SRA (for a paper submission! Yay!). My uploads through http kept timing out ...
RShiny for prototyping + plotting two different user-input variables
Last week after some team meetings I started using RShiny to prototype a webapp for a project I’m working on to show users how many resources (i.e. time, mem...
Building a consensus sequence with vcf files
Note: this post has also been cross-posted to the Center for Computational Biology of Human Disease at Brown, where I currently work. References to Oscar and...
R, Travis-CI, and C++ standards with Ubuntu 16.04
Continuous integration tools like Travis CI are designed to make testing and deploying easier, but often I find myself spending a lot of time and making tiny...
Travis-CI for Python and R with conda
I have been using Travis-CI for about a year or two now, and now that I’ve got it working pretty smoothly and know how to debug it I quite like it. Combined ...
Finally A Website
I’ve had this domain for a few years now with a few different versions in an attempt to make a personal website, but generally I’ve been more interested in p...