@lambdamoses@fosstodon.org
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lambdamoses

@lambdamoses@fosstodon.org

Cultural rebel with rhizomes โ˜ช๏ธ๐Ÿšตโ€โ™€๏ธ๐Ÿด
Spatial -omics, bioinformatics, useR, roadie (starship Voyager) and groadie (starship Wayfarer) cyclista living in Tovaangar (so called LA) without a car for 10 years, Anarcha-Islam. PhD '23 Caltech, BS '17 UCLA #rstats #spatial #bioinformatics #bioconductor #foss4g #cycling #BikeTooter #climatecrisis #actuallyautistic

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Cmastication, to random
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I did some R programming tonight. Unfortunately I died. Still fun.

lambdamoses,
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@Cmastication My parody of the 21st Century Digital Girl song: Twenty-first century digital girl, I don't know how to R but I do my homework. Object of type closure is not subsettable. RStudio crashed, but I don't really care, yeah yeah yeah yeah yeah!

Sorry there's no video of me singing it. Well, maybe I should make one, wearing my %>% shirt and holding my laptop which is full of R hex stickers. https://youtu.be/t5TbEABoPdE

lambdamoses, to python
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I'm thrilled to announce a new preprint from our lab, with in depth analyses showing that Seurat and Scanpy give drastically different results for ostensibly the same data analysis tasks: https://www.biorxiv.org/content/10.1101/2024.04.04.588111v1

ninokadic, to philosophy
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โ€œWe think philosophy is due an ethos change; one where the myth of the โ€˜lone geniusโ€™ is dispelled and where co-authoring is both encouraged and acknowledged.โ€

Link: https://dailynous.com/2021/10/14/co-authorship-in-philosophy-over-the-past-120-years-bourget-weinberg/

@philosophy @academicchatter

lambdamoses,
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@ninokadic @philosophy @academicchatter That's great! To be honest, growing up being fed the lone genius myth in science has contributed to imposter syndrome when I did become a scientist.

lambdamoses, to random
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https://www.science.org/doi/10.1126/science.ade3535

lambdamoses, to random
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R and RStudio are obviously different things. You can use R without using RStudio. Burning question: why do many people conflate the two? I think it's because they have never used R outside RStudio, so they use R if and only if they use RStudio. Anyway, RStudio is so nice, right? It's my favorite IDE. So nice that a colleague of mine uses RStudio as his C++ IDE, and it's not Rcpp.

lambdamoses, to bioinformatics
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Bioinformaticians: If you see an R package in bioinformatics that is in CRAN instead of Bioconductor, does this raise a bit of suspicion? Why or why not?

lambdamoses,
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Well, at least that's better than the wild west of GitHub, right? I still wonder why most R package developers, at least in spatial transcriptomics, don't get their packages to CRAN or Bioconductor.

lambdamoses,
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@Mehrad @Lluis_Revilla think it would be nice to have some regular meetings with users and developers of all walks of life to discuss and build such a standard, if you don't like SCE or AnnData. It's just like standards in hardware and how much trouble lack of a standard causes. For example, in cycling, you can't really mix Shimano and SRAM and newer components are incompatible with older components, so swapping one part causes you to swap many others, even when the others still otherwise work.

lambdamoses,
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@Mehrad @Lluis_Revilla Imagine on a bike ride, you buy a new inner tube to change a flat. Instead of just Presta and Schrader valves which are the standard, you have 10 different standards and need adaptors all the time to inflate the tube and sometimes the adaptors don't work. Many of those valves don't fit in your rim. Isn't that annoying? Rims and tubes conform to Presta or Schrader standards not to give creators of Presta and Schrader valves extra credit. The patents have long expired.

lambdamoses,
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@Lluis_Revilla But I think @Mehrad has a good point. While I personally don't complain about SummarizedExperiment and S4Vectors, how democratic is that decision? And who's in that working group?

lambdamoses,
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@Lluis_Revilla @Mehrad Actually, I think the ranking is problematic, because older packages tend to have higher ranks just because they're older because there has been more time for more people to download them. New packages usually have lower ranking. That's my understanding, correct me if I'm wrong.

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