Genetics and Biostatistics
🎓 New Publication!
Our first paper on Bioconductor training from the Bioconductor Training Committee is now published in PLOS Computational Biology. We're pleased to share our work with the community.
Read here: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012925
Thank you to everyone involved for your contributions!
excited to hear about it tonight. By the way, these calls and the Slack channel are totally open, you can find us via #tidiness_in_bioc on Bioc slack
A bigger post than usual this time, but I wanted to cover as much of the background as I could...
https://jcarroll.com.au/2024/08/11/tidy-dataframes-but-not-tibbles/
{DFplyr} - use {dplyr} functions on an S4Vectors::DataFrame
#datavzrd, our tool for rendering modern interactive, visual, server-free, tabular scientific HTML reports with zero/low-code (https://datavzrd.github.io), now has a tutorial (1-2h): https://datavzrd.github.io/docs/tutorial.html.
We’re brimming with glee to announce the release of bonsai 0.3.0.
bonsai is a parsnip extension package for tree-based models and includes support for random forest and gradient-boosted tree frameworks like partykit and LightGBM.
The 0.3.0 release of bonsai introduces support for accelerated oblique random forests via the "aorsf" engine for classification and regression in tidymodels.
Learn more on the tidyverse blog: https://www.tidyverse.org/blog/2024/06/bonsai-0-3-0/
Made it to Salzburg for #useR2024 ! 🇦🇹 :rstats:
Couldn't be more excited for my Keynote talk on Tues:
💫"Keep R Weird" 🤪
Come for the hexagon pantsuit, stay for the rant about non-standard eval.
(🦭and watch @r_data_table for how to grab dins and some data.table swag after! )
Someone should write a bot for #GitHub Issues, #Slack, etc. that can teach users how to create code blocks.
From user-support experience, it's quite a common problem, where people either send screenshots of code/output, paste it in as-is (which become a rendered nightmare), use inline code, etc. It takes quite a bit of back-and-forth to teach them how to use code blocks.
I was just happy to see that @joss passed 2500 published papers sometime in the last couple of weeks!
This is a nice demonstration of volunteer-run diamond open access succeeding, over about 8 years now.
And we seem to be accelerating, with a bunch of new editors.
Accepted papers per month for this year:
Jan 41
Feb 38
Mar 47
Apr 37
May 51 (a new record for a month!)
Jun 41 (so far)
Tidyomics, a collection of R packages that enable tidyverse-style syntax on biological datasets, is now published:
Thanks to the hard work of the authors especially Stefano!
🚀 Boost Your Bioinformatics Skills!
Join us for the Bioconductor Carpentries RNA-Seq Analysis Workshop!
📅 July 22-23, 2024
📍 Grand Rapids, MI
🔍 Who: Biologists and researchers with some R experience
💡 Why:
- Hands-on Bioconductor training
- Expert instructors
- Networking opportunities
👉 Register now! https://buff.ly/3VdEjj2
#Bioinformatics #Bioconductor #RStats #Carpentries #BioC2024
We have some new instructors at CSAMA this year including Anne-Laure Boulesteix of LMU Munich @BoulesteixLaure and Maria Doyle of University of Limerick and Bioconductor @bioconductor. Organized by Davide Risso @drisso.
CSAMA is a course in Biological Data Science covering analysis of modern molecular data types including single cell and spatial omics.
There is still time to register, please share among anyone you think would be interested.
Information here:
Delighted to announce that a new @nf_core preprint manuscript has just gone live!
A collaboration with #EuroFAANG, the paper covers updates to #Nextflow and @nf_core, and describes the experience of #EuroFaang as they adopted @nf_core.
Let's dive in... 🧵
Understanding Mixed-Effects Models Through Data Simulation https://journals.sagepub.com/doi/full/10.1177/2515245920965119
@bioconductor Thanks core team and developers!
📢 The Bioconductor Core Team is pleased to announce the release of Bioc3.19! A huge thank you to all the developers and community members who contributed to this milestone. Discover all the new packages and improvements in the full release announcement here: https://buff.ly/3Qtjehs 🚀
Very sad news: Our friend and colleague Fritz Leisch passed away this week.
Among his many #rstats contributions:
- Original R Core Team member
- Co-founder of CRAN
- Sweave author for reproducible documents
R Core Team announcement:
https://stat.ethz.ch/pipermail/r-announce/2024/000702.html
BOKU obituary (in German):
Congrats to @naimurashid on being honored with the Grizzle award and giving an amazing lecture on improving replicability of expression signatures for prostate cancer.
So well deserved! 🎉
I can't quite find the words to say how honored I feel to be named ABRF's Mentor of the Year - it is far and away the proudest moment of my scientific lifetime. I feel incredibly privileged every day to get to work with an amazing team of brilliant, hard-working scientists and engineers and to work to give them what they need as they try to make the world a better place full of better science. (1/2)
I'm looking forward to talking about #ResearchSoftware with the University of São Paulo community in about 2 weeks, on 9 May.
