Mike Smith

Research Software Developer at the European Molecular Biology Laboratory.

[Mike Smith @grimbough]

@lakens @deevybee Happy to help, I've battled Bookdown enough to have appreciated a lot of help from others in the past.

Re the figure, do you use Windows? If so, maybe it's case insensitive and was working just fine for you.

[Mike Smith @grimbough]

@lakens @deevybee Looking closer, I think you already have the relevant settings in _output.yml You can just do:

bookdown::render_book(output_format = 'bookdown::pdf_book')

I had to remove \urlstyle{tt} from preamble.tex - will make a pull request for you.

[Mike Smith @grimbough]

@lakens @deevybee If it helps my curiosity got the better of me, so I checked out https://t.co/PtJJQS9Odp and tried out out myself. Looks pretty good! (Hopefully that's the right book🤞)

[Mike Smith @grimbough]

@deevybee and also switched escape=TRUE for some of the kable() tables. Characters like % in a LaTeX table will break the rendering if it isn't escaped.

[Mike Smith @grimbough]

@deevybee FWIW the following gets me a PDF version of your book after I've made a few changes to file name capitalisation.

bookdown::render_book(
output_format = bookdown::pdf_book(
latex_engine = "xelatex"
)
)

[Mike Smith @grimbough]

Great opportunity to keep up-to-date with Bioconductor, and meet other users and developers.

Also, Ghent is beautiful.

[Bioconductor @Bioconductor]

📣 The #Bioconductor EuroBioc 2023 conference will be in Ghent, Belgium 🇧🇪 on the 20, 21, 22 September 2023 🎉

More details, keynote speakers and calendar at https://t.co/dqFbAAN9IK

Oh, and abstract submissions are already open!

#rstats #Bioinformatics

[Mike Smith @grimbough]

Since we're updating Modern Statistics for Modern Biology to use #QuartoPub, I thought I'd detail how I added anchor links to our equations.

https://t.co/i6v21AladJ

[Mike Smith @grimbough]

@jo_rainer @its_JPhilipp First time for everything😬

[Mike Smith @grimbough]

@robinson_es I don't know what a luggage sleeve is, but otherwise these are pretty great https://t.co/oFrVjlOIXK

[Mike Smith @grimbough]

Abstract submission closes 31st May.

Travel scholarships are available; apply as part of the abstract submission process.

[Mike Smith @grimbough]

@WeAreRLadies Also a big shout out to @jo_rainer who designs some awesome stickers for our events.

Here's my home town of Heidelberg in hex sticker form

[Mike Smith @grimbough]

@WeAreRLadies There's some pretty great ones in the Bioconductor collection https://t.co/DwDOQL9TyG

Here's a few animal themed packages/stickers

[Mike Smith @grimbough]

Any #RStats users know what setting I need to change to not have blurry, drop-shadowed, code in the new syntax highlighted help pages? This makes my eyes hurt.

Currently using RStudio with the Cobalt theme.

[Mike Smith @grimbough]

@CedScherer @R4DScommunity @rstudio To me the explosion in v4 doesn't look quite so dramatic compared to e.g. v3 in March 2020 using raw counts.

Those alternative labels are included as is. They make up the bottom 4 colours in the stacked bars, and don't really look significant to me.

[Mike Smith @grimbough]

@CedScherer @R4DScommunity @rstudio Would be interested in seeing the smoothing. I see a similar but different pattern in the the counts.

Drop in proportion of unique IPs suggests automated process responsible for increase downloads, maybe CI or similar.

Code: https://t.co/F0H0KlFM2J

[Mike Smith @grimbough]

@NicolaMTomas @wolfgangkhuber @FlorianIngelfi1 @mt_morgan @drisso1893 @jo_rainer @CSoneson @const_ae @its_JPhilipp Yep, you can find more details at https://t.co/Pew0fY9KHC

[Mike Smith @grimbough]

@TimPollington @Bioconductor @rdrrHQ That Github org is for projects actually managed by @Bioconductor (infrastructure packages, website, build system etc)

You can view the package source at: https://t.co/FWKRdnaUia

Looks like there's only one vignettes and that's also rendered at: https://t.co/TXMn4VGpJ3

[Mike Smith @grimbough]

@henrikbengtsson @Bioconductor Agreed, although you can now look at this to get a quick overview https://t.co/COsdH9cXd8

[Mike Smith @grimbough]

Do you have some #rstats scripts that you've always wanted to make into a @Bioconductor package, but the gap from scripts to a package seems daunting?

Apply to the new mentorship program for the chance to get help making that leap.