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rmflight, to LEGO
@rmflight@mastodon.social avatar

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
@rmflight@mastodon.social avatar

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
@rmflight@mastodon.social avatar

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,
@rmflight@mastodon.social avatar

@brodriguesco I've done that for packages, but not generally python versions.

Someone else suggested pyenv to give a custom version of python and packages, I will probably end up trying that.

brodriguesco,
@brodriguesco@fosstodon.org avatar

@rmflight yes exactly pyenv also allows you to choose python version afaik

rmflight, to random
@rmflight@mastodon.social avatar

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/

njtierney,
@njtierney@aus.social avatar

@rmflight @grrrck Oh that's so cool!

rmflight, to random
@rmflight@mastodon.social avatar

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
@rmflight@mastodon.social avatar

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

Very nice.

grrrck,
@grrrck@fosstodon.org avatar

@rmflight I’ve really been enjoying @phanpy! It also has a really nifty “Catch-up” feature

grrrck,
@grrrck@fosstodon.org avatar

@rmflight @phanpy ooh, thanks to that post, I just learned it also makes adding an image description just part of writing the post! And it warns you if you’re boosting or quoting a toot with an image that doesn’t have a description.

rmflight, to random
@rmflight@mastodon.social avatar

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
@rmflight@mastodon.social avatar

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. 🤦‍♂️

Mehrad,
@Mehrad@fosstodon.org avatar

@rmflight
Happens to the best of us. I have something around 35 scripts that contains QoL functions. Now I have a small wrapper that measures time for every script and output it as a sorted knitr markdown table. Perhaps that can help you spot issues whenever you update those scripts.

rmflight, to random
@rmflight@mastodon.social avatar

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.

hrbrmstr,
@hrbrmstr@mastodon.social avatar

@rmflight The "supersons" (or whatev the movie with superman batman and their kids are on streaming" was oddly decent both in terms of dialogue and animation.

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr a lot of the DC animation I've watched has been pretty decent, honestly. Didn't watch that particular one before I let my Max subscription end, unfortunately.

Also just realized that I didn't finish watching Ponyo, either. 😬

rmflight, to random
@rmflight@mastodon.social avatar

A stuffed Axolotl from my family for Christmas! It's so cute!

rmflight,
@rmflight@mastodon.social avatar

@thepoliticalcat nope. Just think they are interesting creatures.

rmflight, to random
@rmflight@mastodon.social avatar

Stopped DS9 episode so I could go to bed. In the time I scrolled Reddit since then, I would have finished the episode. 🤦‍♂️

rmflight, to random
@rmflight@mastodon.social avatar

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. 😭

Cmastication,
@Cmastication@mastodon.social avatar

@rmflight at least you didn’t do it with your pants on backwards

rmflight,
@rmflight@mastodon.social avatar
rmflight, to random
@rmflight@mastodon.social avatar

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 🤷

jonny,
@jonny@neuromatch.social avatar

@rmflight
I made a version using Carl's code for Jekyll: https://github.com/sneakers-the-rat/sfn23/blob/main/_includes/comments.html
https://github.com/sneakers-the-rat/sfn23/blob/main/_sass/comments.scss

And was planning on turning it into a plugin. I could def take a shot at making it work for quarto - the js is self contained and super straightforward.

rmflight, to random
@rmflight@mastodon.social avatar

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?

hrbrmstr,
@hrbrmstr@mastodon.social avatar

@rmflight the GOP spreads that around (tho they are usually less kind than to use the words "legally vote") to gin up conflict and confuse the morons in their party.

rmflight, to random
@rmflight@mastodon.social avatar

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.

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