Category Archives: Computer tutorials
Alignment and phylogenetic inference with hmmalign and RAxML-ng
RAxML is one of the most popular programs around for phylogenetic inference via maximum likelihood. Similarly, hmmalign within HMMER 3 is a popular way to align amino acid sequences against HMMs from Pfam or created de novo. Combine the two … Continue reading
A short tutorial on Gnu Parallel
This post comes form Luke Piszkin, an undergraduate researcher in the Bowman Lab. Gnu Parallel is a must-have utility for anyone that spends a lot of time in Linux Land, and Luke recently had to gain some Gnu Parallel fluency … Continue reading
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Finding those lost data files
It’s been a long time since I’ve had the bandwidth to write up a code snippet here. This morning I had not quite enough time between Zoom meetings to tackle something more involved, so here goes! In this case I … Continue reading
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Tutorial: SuperSOMS and an R script for detecting regions of interest
A common exercise in environmental microbiology is counting bacterial cells with an epifluorescent microscope. During my PhD I spend many hours hunched over a microscope in a darkened room, contemplating which points of light were bacteria (and should thus be … Continue reading
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Tutorial: Self Organizing Maps in R
Self-organizing maps (SOMs) are a form of neural network and a wonderful way to partition complex data. In our lab they’re a routine part of our flow cytometry and sequence analysis workflows, but we use them for all kinds of … Continue reading
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Tutorial: Nanopore Analysis Pipeline
Introduction Hi! I’m Sabeel Mansuri, an Undergraduate Research Assistant for the Bowman Lab at the Scripps Institute of Oceanography, University of California San Diego. The following is a tutorial that demonstrates a pipeline used to assemble and annotate a bacterial … Continue reading
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Weighted Gene Correlation Network Analysis (WGCNA) Applied to Microbial Communities
Weighted gene correlation network analysis (WGCNA) is a powerful network analysis tool that can be used to identify groups of highly correlated genes that co-occur across your samples. Thus genes are sorted into modules and these modules can then be … Continue reading
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Tutorial: How to make a map using QGIS
Hi! I’m Natalia Erazo, currently working on the Ecuador project aimed at examining biogeochemical processes in mangrove forest. In this tutorial, we’ll learn the basics of (free) QGIS, how to import vector data, and make a map using data obtained from … Continue reading
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So you want to use your computer for science…
It’s been a while since I was a new graduate student, and I’ve forgotten how little I knew about computers back then. I was reminded recently while teaching a couple of lab members how to use ffmpeg, an excellent command … Continue reading
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Analyzing flow cytometry data with R
We recently got our CyFlow Space flow cytometer in the lab and have been working out the kinks. From a flow cytometry perspective the California coastal environment is pretty different from the western Antarctic Peninsula where I’ve done most of … Continue reading
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