Tutorial

2022-12-22 Polyglot Jupyterlab setup

A quick-start list of commands for a fully-configured Jupyterlab user install that supports bash, R, and python.

2022-07-20 Conda and bash startup files

Below is an example bash configuration that allows conda (and other similar tools) to operate in all types of bash shell, including non-interactively.

2022-03-21 Improving QR code recognition: an experiment

With a few very simple and automated image manipulations (scaling, sharpening, and blurring), we can dramatically improve the rate at which barcodes can be recognised.

2022-01-11 Git annex worked example

This is a tutorial for the Weigel group’s difflines project. I use difflines analyses here so that our group has concrete examples to work with. Obviously none of this will work for you as-is if you’re not part of our group, but hopefully this is helpful by analogy.

2021-10-25 Git annex: an aide to collaborative reproducible analyses

Git has been a revolutionary tool for online collaborative software development. Git annex extends git’s abilities to track and share large files in addition to code. Together these tools enable effective collaboration on large bioinformatics analyses.

2021-07-07 Metadata, and how to tame it

AAAARRRRRGH!! Metadata herding remains the most frustrating aspect of genomic metaanalyses. Here are some lessons learned from several large ongoing natural variation genomics (meta)analyses I am involved in.

2020-10-09 Spatial Population Genomics and Landscape Genomics: a lightning tour

A brief introduction to concepts in Population and Landscape genomics, originally given as a talk at the Weigel lab.