bioinformatics

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.

2022-01-11 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.

2021-05-24 Enable conda on NCI’s Gadi

NB: this post has been superseded by my more recent post on conda and bash configuration

Gadi’s shell system and conda init interact poorly, requiring one to use login shells (bash -l) in PBS jobs to be able to access conda.

2021-05-06 How to Extract Points From Raster in R

To extract e.g. bioclim variables from worldclim.org raster files, use raster::extract.