@rmflight@mastodon.social avatar

rmflight

@rmflight@mastodon.social

Research parasite* @universityofky. Interested in #openscience, #rstats, bioinformatics, #datavis he/him

*One who uses others data to conduct research, both publicly available data, and those from direct collaborations.

#fedi22

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rmflight, to LEGO
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6 won't sit through an entire Star Wars movie, but appreciates some of the droids they have to fight.

Anyone recognize what this is?

A deployed Lego droid

rmflight, to bioinformatics
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What RNA-Seq datasets are everyone using for RNA-Seq differential analysis workshops, using {DESeq2} or {limma} ?

Two or three categories, and ideally a good (4 or 5+) number of replicates, human or mouse?

We have some new methods in ontology enrichment, and we really could use some more datasets to try them on.

I've found the {airways} dataset, and lung adenocarcinoma from {recount3} (as an easy pull). Looking for others. TIA.

rmflight, to python
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Kind of thankful that is not a system dependency that is pretty much embedded in the OS, and that I can upgrade it even on older software (like running R 4.3.0 on Ubuntu 20 LTS) without worrying about other things depending on it.

In contrast to 3.6, that I'm not keen to try and force an upgrade to 3.8 so I can get access to a newer version of SciPy that exposes some underlying functionality that one of our python packages depends on.

rmflight, to random
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After @njtierney reviewed one of my packages, and commented on DESCRIPTION white space style, I decided to revisit read.dcf and white space in my pre-commit hooks.

Which also had me reviewing @grrrck modifications to the hooks they had made in a fork to keep automatic from overriding a manual change, and updated the hooks.

Now the hooks live in an actual GH repo instead of gists, hopefully making them easier to find for others.

https://github.com/rmflight/r_git_hooks/

rmflight, to random
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Did something change in recently (last couple of years) for comparing two logical vectors?

I'm pretty sure this used to work, and return the expected single value logical:

v1 = c(TRUE, FALSE)  
v2 = c(TRUE, TRUE)

v1 == v2 # FALSE

Now I have to do:

identical(v1, v2)

Like, I'm going to be checking all of my package code to check for logical comparisons using ==, because it's definitely not doing what I expect anymore.

rmflight, to random
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Oho! I just noticed @phanpy now gives me the option to either "boost" or "quote"!

Very nice.

rmflight, to random
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is awesome, and I am finding myself using it more and more over for based reports and documents. I definitely recommend checking out the new features in v 1.4!

https://fosstodon.org/@Posit/111813004531309642

I will note one pain point, and that is tables with captions in Word documents. If you want or need that, it's still not quite there, unfortunately (and it's being worked on, I keep an eye on the issues on GH). Here's hoping we get it in v 1.5!

rmflight, to random
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For the past 6 months or so, I've just been living with the fact that sourceing my function file directory takes 90 seconds at the beginning of this analysis.

Today, I got annoyed enough I decided to actually measure the time it takes, and figure out if any specific file was causing the long delay.

Turns out, I had left a data processing script meant to be run once in the function file directory! Moved it out, and now it's 1 second to source everything. 🤦‍♂️

rmflight, to random
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Finally watched "League of Superpets". Honestly, a better Justice League movie than Joss Whedon's version, and almost up there with Zach Snyder's. I would definitely watch the sequel.

rmflight, to random
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A stuffed Axolotl from my family for Christmas! It's so cute!

rmflight, to random
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Me, 44 yo, having some ankle issues that have been slowly clearing up.

Spouse says 5's shirt was "criss-cross".

My brain goes: "Kris Kros'll make ya jump, jump", and I jump.

My ankle immediately regrets it. 😭

rmflight, to random
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So who is going to give this a try w/ blogs?

Some neat javascript to use :mastodon: as a comment engine, at these two links.

https://carlschwan.eu/2020/12/29/adding-comments-to-your-static-blog-with-mastodon/

https://anarc.at/blog/2023-01-19-mastodon-comments-in-ikiwiki/

utterances et al already require a GH account, :mastodon: definitely feels like a more natural fit, especially where you use the toot announcing the blog post as the anchor.

Yes, it would potentially require publishing twice (first for link, second to add masto post ID), but 🤷

rmflight, to random
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I'm always surprised by the number of people who assume that permanent residents / landed immigrant / green card holders are allowed to vote (USA).

I like to encourage people I know to go and "vote well, because I can't", and I get funny looks because they are under the impression that I can vote. It gets even better when they discover I pay the same taxes as a citizen, and still can't vote.

Where is this misinformation that non-citizens can legally vote?

rmflight, to random
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Does anyone know if there is a built-in size limit on square matrices passed to svd?

I have some 30K x 30K matrices I want the inverse of, and therefore am using stats::svd and some matrix multiplication to do it.

n_val = 30000  
tmp_matrix = matrix(rnorm((n_val ^ 2) / 2), nrow = n_val, ncol = n_val)  
svd_res = svd(tmp_matrix)

I get a segfault, with invalid permissions for the memory. Actual RAM usage seems fine (64 GB machine).

Google (and kagi) aren't helping here.

rmflight, to random
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Driving companion today. Kids were insistent that I bring a stuffy with me on my solo speed run to Dad's to get stuff that's been sitting in his basement for 13 years.

Doesn't complain about anything, not much for conversation though.

rmflight, to machinelearning
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Two new preprints on and now available from our lab!

Both are centered around learning / predicting metabolite - to - pathway relationships in KEGG.

A cautionary tale about properly vetting datasets used in supervised learning predicting metabolic pathway involvement
https://www.biorxiv.org/content/10.1101/2023.10.03.560711v1

Benchmark dataset for training machine learning models to predict the pathway involvement of metabolites
https://www.biorxiv.org/content/10.1101/2023.10.03.560715v1

/1

rmflight, to random
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My search foo is failing me.

@hrbrmstr had a Daily Drop post highlighting a variety of methods for enabling parallel processing not that long ago??

I cannot find the drop in my email, or on substack, or in my bookmarks here, which is really, really odd, b/c I commented on it even.

Help?

rmflight, to random
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Unfortunately have to miss @Cmastication keynote: "It's Abstractions All the Way Down"

at due to cooking lunch for the fam, but looking forward to checking it out later (hopefully tomorrow sometime after the recording is in the conf portal).

rmflight, to random
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Anyone else overly amused that the first day of actual talks are on "talk like a pirate day"? 🤣

rmflight, to random
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PLOS-One has a survey about requiring code for publishing articles if you would like to leave feedback.

https://survey.alchemer.com/s3/7500690/Code-Sharing-Policy-Survey-2023-ONE

rmflight, to random
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Was wondering why every iteration of my code was spitting out a message in this code:

if (iter %% 1000) {  
 message(...)  
}

Took forever to realize I wanted:

if ((iter %% 1000) == 0) {  
 message(...)  
}

🤦‍♂️

rmflight, to random
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I know it's at least 1/2 the talking, but I'm done with this trip, and so want to turn tail for home instead of my in-laws tomorrow.

One more week, and then maybe (big maybe) a stop at Lego Discovery center just outside DC on our way back home. We are all so tired, and another week is just going to add onto it.

rmflight, to random
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One day down, 1 1/2 to go.

Safe in Pennsylvania for the night. Started at 8am, finally stopped at 6:10pm.

Had an accident to get around on I81N, that added a bit, but wasn't too badly. Maine bound tomorrow I think.

rmflight, to random
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This will either work great, or be a disaster. Trying something different, and mapping our route out with stops, and making the reservation a day in advance.

So actually shooting for close to 8 hours of driving time tomorrow, stopping in Harrisburg PA tomorrow, and have an actual reservation at a hotel.

rmflight, to random
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Definitely an adult. Excited for a new salad spinner after the old one broke.

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