Articles by tag: bioinformatics

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.

Creating simple genome annotation tables

Working with annotated genomes is not always an easy process. Here, I detail how to easily create tabular annotation data from GENCODE that can be easily used in any analysis.

A fully-fledged toolchain for Rust on Windows

Rust is rapidly becoming a powerful and popular programming language. Running it on Windows can be a bit of a pain, so here's a guide to make it easier.

Creating a custom genome annotation for HiGlass

HiGlass is an interactive genome browser that's particularly useful for Hi-C data. Here, I describe how to create your own genome annotation file for HiGlass, allowing you to more easily display your work, regardless of the organism you work in.

Pragmatic guidelines for bioinformatics software tools

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

"Support" over "coverage"

"Read coverage" in high throughput sequencing is a bit of an ambiguous term. Here, I make the argument for using the analogous term "support", coming from set theory and its interpretation.

The woes of using bioinformatics software: a case study in trying to install ChAMP

Making high-quality bioinformatics software is hard. Installing and using it shouldn't be, though. Here's a detailed description of all the work I did to try and install the ChAMP package.

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.