What RNA-Seq datasets are everyone using for RNA-Seq differential analysis workshops, using {DESeq2} or {limma} #RStats?

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.

#bioinformatics #RnaSeq

Don’t want your matrix becoming a lonely vector if you index a single column? There is a simple solution 👇

Discovered this gem ages ago – couldn't believe I didn't know about it sooner though.

Hope this ripper helps someone else.

#RStats

Hey, #rstats champions! Sometimes you might want to consider reordering 🔀 your boxplot groups to more clearly illustrate the differences between them. You can easily achieve this with the `reorder` function within your aesthetic mappings. Check out my blog for a full working example and code.

🔗 https://lpembleton.rbind.io/ramblings/R/#order-a-boxplot-for-improved-across-axis-comparisions

earthdatalogin by Carl Boettiger streamlines the process of accessing NASA data from the Earth Data cloud program.

It also has a few vignettes explaining "Data Cubes with STAC", "Cloud-Native Access", and even shows how to read some data from a 31 Terrabyte Zarr.

https://boettiger-lab.github.io/earthdatalogin/

#rstats #rspatial #gischat

At my workplace, we're looking into how we can support the processing of very large datasets in R. It would be wonderful if some bioinformaticians could answer a couple of questions to direct us to the problem points.

We're hoping that we can publish something out of this that will be helpful to everyone in the field: https://forms.office.com/r/jNd2cbEZkh

#rstats #bioinformatics

I'm looking for a reviewer for an #RStats package, {rangr}, https://github.com/popecol/rangr, a species range dynamics simulation toolset for @rOpenSci. I have one review completed and need one more. If you're interested please contact me via DM and let me know.

The review already in process can be found here on our GitHub repository for software reviews,
https://github.com/ropensci/software-review/issues/595.

GitHub - popecol/rangr: Species range dynamics simulation toolset

Species range dynamics simulation toolset. Contribute to popecol/rangr development by creating an account on GitHub.

^GitHub

(1/2) Timetk for Python 🚀🚀🚀

The timetk, one of the main R packages for time series analysis and forecasting ❤️, by Matt Dancho, is now available in Python 🐍. The package provides a variety of tools for working with time series data and analyzing it. The Python version leverages pandas for processing time series data and plotly for visualization.

#timeseries #python #rstats #forecasting #DataScience

Cool #RStats prokect alert!

https://github.com/r-wasm/webr

GitHub - r-wasm/webr: The statistical language R compiled to WebAssembly via Emscripten, for use in web browsers and Node.

The statistical language R compiled to WebAssembly via Emscripten, for use in web browsers and Node. - GitHub - r-wasm/webr: The statistical language R compiled to WebAssembly via Emscripten, for u...

^GitHub

I'm wanting to incorporate some #Rstats in my university #Evolution class so that students learn/reinforce some R skills while increasing their understanding of evolution. I did an internet search and found next to nothing:

Too advanced:
https://www.mimuw.edu.pl/~lukaskoz/teaching/sad2/books/Analysis_of_Phylogenetics_and_Evolution_with_R.pdf

Interesting, but pretty limited in what it does:
https://onlinelibrary.wiley.com/doi/10.1002/ece3.5412

Any recommendations?

Last Wednesday I ran @joelnitta's excellent "Introduction to Targets" workshop and taught around 15 people how to write workflows in R. I also tested out some bonus content about running targets on Slurm/HPC which I hope to get included in the workshop eventually.

All the feedback was positive, so I recommend giving it a shot if you're interested in teaching Targets at your organization!

https://github.com/carpentries-incubator/targets-workshop

#rstats #targets

GitHub - carpentries-incubator/targets-workshop: Pre-alpha {targets} workshop

Pre-alpha {targets} workshop. Contribute to carpentries-incubator/targets-workshop development by creating an account on GitHub.

^GitHub

New resource: a set of miscellaneous general-purpose R functions. I created most of these functions for my own personal use over the past 13 years, but I have also shared them informally with many students, friends, and colleagues. I have decided to publish them for anyone else who may be interested. They address a variety of tasks that sometimes come up in psychological data analysis.

https://saraemilyburke.com/stats/miscfunctions.html

#Statistics #RStats

New release of `plot2` coming in hot. As a reminder, the plot2 📦 provides a lightweight extension of the base #rstats plotting system. Automatically handles grouping and legends, etc. This version also adds support for pointrange and ribbon plots.

Make those base plots look good with minimal effort: https://github.com/grantmcdermott/plot2

New version of the rotl #rstats package. This package allows you to retrieve phylogenetic trees from the Open Tree of Life API.

The only change is that the function to match taxonomic names returns the taxon with the highest score if there are multiple matches. The score represents the distance to the match (a perfect match has a score of 1.0)

* Repo: https://github.com/ropensci/rotl
* CRAN: https://cran.r-project.org/package=rotl

@phenidone @andreasdotorg @mcc @andy_twosticks

My most recent disappointment with garbage collection involves R and `tidyverse` pipes on some large-ish transit data in an 8 GB laptop. By breaking the pipe chains into single steps and forcing a garbage collect after each step I was able to run it.

#RStats

This week in #TidyTuesday we look at the Portal Project.

Thanks to: @ethanwhite for the data.

The project: https://portal.weecology.org / @weecology

Code: https://github.com/mvbloois/tidytuesday

#dataviz #rstats