Articles by tag: comp-bio

Understanding file permissions

Here is a brief rundown of file permissions on Unix systems and how to change them.

General purpose Anaconda tips

I use Anaconda managing my computational software environments. Here are some pragmatic tips for making conda environments easier to deal with.

A solution to dependency hell: static binaries by default

Dependencies are complicated for computational biologists. Adapting a different development strategy can help your end users.

Aggregate peak analysis with Hi-C data

Hi-C data analysis is still a relatively new field in genomics. The data itself is quite large and expensive to make, which means datasets and exploration of the data is still immature, compared to other technologies like RNA-seq. Here, I discuss aggregate peak analysis, a commonly-used and poorly-documented analytical technique to verify identified features in Hi-C data.

What is differential analysis, anyway?

Differential analysis using sequencing data is, at its heart, a very simple idea that involves a lot of complicated statistics. It makes explaining the simple idea to newcomers in bioinformatics very difficult. Here, I want to break down the motivation behind differential analysis and explain where the complicated statistics come from.

Please, show your work

How incomprehensible machine learning models answer questions without providing the solutions we desire.

Now is an exciting time for mathematicians in the biological sciences

There are many reasons to be excited about scientific progress in the biological sciences, especially if you're a mathematician of almost any kind.

Pragmatic guidelines for bioinformatics software tools

I offer 10 practical suggestions for designing robust, intuitive, and user-friendly software tools for bioinformatics.

Building Conda Packages

A brief introduction to creating your own conda packages.

How I Maintain a Reproducible Computational Environment

A brief description of how I try my best to keep a low-maintenance and reproducible software environment.