Making a bubble plot to show frequencies
<p>I've been using ggplot2 in R to make a bubbleplot, to show frequencies. This is an alternative to a histogram. Here's a little example:</p><p> I have a file year_data_file_example.txt with col...
Furtress of solitude
In the Pilbara region of Western Australia lives the western pebble mouse ( Pseudomys chapmani ), a rarely seen rodent that excavates a complex subterranean burrow system in the rocky substrate. These...
The Mentorship Index
Background...
Vibe coding with SEraster and STcompare to compare spatial transcriptomics technologies
Introduction...
Using MOB-suite to predict plasmids in bacterial genome assemblies
<p>Today I wanted to predict plasmids in a bacterial genome assembly, and used the <a href="https://github.com/phac-nml/mob-suite">MOB-suite</a> tool.</p><p>Here's how I ran it on the Sanger...
The Quickening
In a paper titled “THEOREMS FOR A PRICE: Tomorrow’s Semi-Rigorous Mathematics Culture” published in 1993, mathematician Doron Zeilberger wrote: There are writings on the wall that, n...
Creating custom (non-Font Awesome) icons for a Jekyll-based website
This one is pretty niche even by my standards. Notes largely for my own benefit, but they may be useful if you: I’ll assume that you have git-cloned jekyll-theme-chirpy, run bundle and are able ...
State of the Blog
<p>ChatGPT came out in November 2022 and it has completely changed the Internet. In my post Learning about ChatGPT via ChatGPT I had prompted: "Will ChatGPT replace Google?" to which the model back th...
Using enadownloader to download fastqs from the ENA
<p>I wanted to download fastq files for a long list of SRR accessions from the <a href="https://www.ebi.ac.uk/ena/browser/home">ENA</a> today.</p><p>I realised I could use the <a href="https://av...
ONT read QC strategies for assembly
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