Discover and read the best of Twitter Threads about #bookdown

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Morning! Let's continue with the polling results, today and get some #learningtips. Here is what people voted for regarding learnings strategies! Not surprisingly, the big majority likes some hands-on exercises, although a mix between theory and practice is also welcome 😎 Results to poll about learn...
📚 Very few people voted for learning from books about coding, but have you already seen all the resources out there? #rstats has a big pile, and the best way to browse them all is with the Big Book of R #rmarkdown #bookdown
Most of the people like blogs and written content. Well this is the perfect opportunity to point you to the #RLadies blogs collected by @PipingHotData & @DrMowinckels
Read 4 tweets
Interested to learn about #tidyverse?

Happy to share that @JHUDataScience just released a 5 course Specialization on @Coursera:

Tidyverse Skills for Data Science in R! 🎉…

#rstats #dataviz #datascience #statistics @jhubiostat @JohnsHopkinsSPH

A 🧵 1/n
First, I wrote a blogpost giving a few highlights about the Specialization, what someone will learn, and a bit about the instructors who built the series: @mirnas22 @Shannon_E_Ellis @rdpeng and me! 👩‍🏫👨‍🏫…

The first course, Introduction to the #Tidyverse, begins with what are "tidy" data, how this helps data organization, how non-tidy can be transformed to tidy data, the data science project life cycle, and an overview of the #tidyverse ecosystem!

Read 13 tweets
Excited to finally share my Jupyter Book course template!…

In just 3 steps you can have your very own course website deployed and ready for your Jupyter Notebooks and markdown content! 😅whew!

Thanks @ProjectJupyter and Executable Books project! Image
To be clear, I am only a USER of the project - all credit to the devs.

It really is just two steps! Here is the repo template:…

(Thanks @TBeuzen for the assist with the GH Action!) Image
I’ll highlight a few features of this template repo that may be useful for teaching:

1. Support for executing code in a browser using thebe and @mybinderorg!

In an online class, you can do live code cell execution in Python-students can follow along with no setup on their end! Image
Read 9 tweets
If you are interested in analyzing #SingleCell #RNAseq data in #Bioconductor using #rstats, please check out our paper Orchestrating single-cell analysis (OSCA) with @Bioconductor that was published in @naturemethods this week! #genomics #scRNAseq #dataviz #methodsmatter
@Bioconductor @naturemethods OSCA is a rich, reproducible, accessible (from beginners to experts!) resource with many #scRNAseq workflows & datasets. The resource is an online #bookdown book that compiles every night to track development by the open-source and open-development @Bioconductor #rstats community
@Bioconductor @naturemethods Now, OSCA is not the only set of packages / workflows for the analysis of #scRNAseq data. #Scanpy ( and #Seurat ( and are two incredibly popular packages in #python and #rstats, respectively.
Read 9 tweets
1. PhD thesis 'Modelling BCG vaccination in the UK: What is the impact of changing policy?' submitted and everything is totally normal....

Written with #rstats, #bookdown, and #thesisdown.

Read here:

#phdchat #epitwitter #openscience #tuberculosis
2. Thanks to my supervisors @n3113n and @Christensen_H + my funders @HPRU_EI + @PHE_uk for the data.
3. Some results: 'getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data'



Read 13 tweets
Someone asked me recently what resources I’d recommend for furthering one’s introduction to Bayesian statistics after going through @rlmcelreath's text (…) and my accompanying project (…).

Here are my thoughts:
It probably goes without saying, but just in case you missed it, make sure you check out McElreath’s lectures on his text, too…. He has three semester’s worth and they’re overall really great.
And plus, I also like his sand-alone lecture on “Bayesian Statistics without Frequentist Language” . It’s more conceptual than applied, but we could all probably do with a little more philosophy of statistics in our lives.
Read 18 tweets
The writing phase of my PhD has begun. I am writing it in @rstudio using @xieyihui excellent #bookdown package. I am hosting it live on as I write. Any and all criticisms, tips and encouragements are appreciated. Daily commits. Here goes nothing.
Next step is to sort out citation issues, and figure out how to keep protected data off github while still being able to use it in the bookdown rendering
A few hours of troubleshooting later: @mendeley_com's bibtex generator turned out to create a duplicate entry with same citation key for same journal article in the My Library and in a Group I was a part of. No indication that this would happen. Error only occured with...
Read 5 tweets

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