A microbiologist with a data science problem

2020-May-04

Making FiveThirtyEight-like tables in Jupyter with Jinja2 and Pandas

I love the tables on FiveThirtyEight. I often want to similarly visualize a Pandas DataFrame …

2015-August-12

Making trees in the Jupyter notebook (part 2 - Bokeh)

This post will work with the tree and information we produced in the last post …

2015-August-07

Making trees in the Jupyter notebook (part 1 - IToL)

Let's extend the previous post by scraping the CAZy website for accession numbers from genes …

2015-August-02

Using rvest to scrape the CAZy website

I have been looking for a nice excuse to play with rvest and since we're …

2015-April-20

Melting your phyloseq object with dplyr/tidyr

If you're a microbial ecologist and you haven't used phyloseq, put away your vintage scarf …

2015-April-17

Evaluating 515F primers

Before we begin, I stumbled across this really great blog post from the Knight lab …

2015-April-14

Exploring 515F primer targets in archaeal and bacterial SSU rRNA genes

Microbial ecologists have long considered the 515F SSU rRNA gene PCR primer to be "universal …