WordPress Management

I’ll keep this quick It’s my third lab notebook post of the day, so definitely want to be brief with all this! But basically, I’m taking over the Bitter Crab blog from Grace! I’ve got a bunch of vague ideas for where to go from here, with the goal of keeping it generally outreach-y rather than getting too tied up in what’s happening in the lab. After all, if people want that, they can just come here! I also already wrote my first blog post – on snow and Tanner crab hybridization! Anyways, this is largely to mark that a) I’m managing the blog now, and b) to just put down some ideas I had for future articles to write. They’re generally Tanner- or Hematodinium-centric, but branch out a bit into some other Alaskan crab fisheries. They are as follows: Tanner crab fisheries (Bering Sea, Kodiak, SE) Tanner crab mating…

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Manual Clustering 2

Manual Clustering, Continued Alright, some updates from last time: Rather than setting the number of modules independently for each individual crab/transcriptome, I specified a single cut height, which was used on the dendrogram for each crab to separate into modules. For crabs A-F (where three time points are present), this cut height was 1.8, and was chosen because it generally separated crabs into 5-8 modules, all of which appeared to contain single expression patterns. Crabs G, H, and I were part of the elevated-temperature treatment group, which only had 2 time points, and so that cut height just wasn’t adequate. As a result, for these crabs, I bumped up the cut height to 10. These changes can be seen in scripts 71-73. All are the same except for initial inputs and module naming but here’s one as an example I changed my name scheme for the manual clustering method. Previously,…

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Using Linear Modeling on Hematodinium

Quarter Recap Before getting into the details, the GitHub repo for all this is available here! It also includes a more detailed write-up here So this quarter, I took Sarah Converse’s QERM 514 class on linear modeling. As the final project, we chose a data set to model. My choice was, naturally, some data on Hematodinium and Tanner crab – specifically, I chose the 2007-2012 Southeast Alaska Tanner crab survey data we obtained from Pam Jensen. For these surveys, each row equals one crab, with approximately 14,500 crab in our dataset total. A variety of physical and environmental factors are tracked – most notably, the following: Hematodinum infection status (infected or uninfected) Year Location code Day and time Pot depth Carapace width Sex Shell condition Black Mat disease infection status Missing legs code Of these, I treated year, carapace width, day, and pot depth as continuous, and all others as…

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