Today I learned how to use Pagès’s awesome {DelayedArray} @bioconductor package to handle gene expression data stored in parquet files. https://tomsing1.github.io/blog/posts/parquetArray/ This way, I can leverage familiar R tools and take
advantage of the language-agnostic parquet file format, querying very large gene expression datasets. Do you have experience with parquet files for biological data - please share the lessons you have learned! #til #parquet #rstats #duckdb #bioconductor

v2 added suppl. note on how Seurat and scanpy give wildly different log fold changes, why their log FC implementations are wrong (Lior Pachter and Nicolas Bray), and how VoyagerPy has consistent results as scran (R Voyager workflow). I have also added suppl. tables comparing Voyager and similar packages such as Seurat, squidpy, Giotto, and STUtility/semla. Please let me know if you have questions or feedback! #rstats #python #spatial #bioinformatics #bioconductor https://doi.org/10.1101/2023.07.20.549945

Space, the current frontier. These R the voyages of R package Voyager, which brings the glorious tradition of geospatial exploratory spatial data analysis to spatial -omics. Here's v2 of the preprint, which describes the Voyager project, show some case studies e.g. negative spatial autocorrelation in tissue, and compatibility tests showing consistent results from the R and Python implementations of Voyager. #rstats #python #spatial #bioinformatics #bioconductor https://doi.org/10.1101/2023.07.20.549945

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? #bioconductor #bioinformatics #rstats

Space, the current frontier. These R the voyages of the R package Voyager. Finally the preprint is out: https://www.biorxiv.org/content/10.1101/2023.07.20.549945v1?ct= #rstats #bioconductor #python #spatial #bioinformatics @bioconductor

Quick update on our #Bioconductor redesign survey. Some regions are underrepresented (see https://bit.ly/biocwebsite), and we need your help!

Take or share our survey to help make Bioconductor more inclusive and user-friendly.🌍🌎🌏

Survey closes this Friday June 23rd. Link: https://t.maze.co/169169456

#bioinformatics #RStats #OpenScience

#Bioconductor はウェブサイトの再設計のためにみなさんの意見を伺いたいと思っています。 http://t.maze.co/169169456 でその意見を入力していただけます。 (締切は6月23日になります。)
気楽にご入力ください！

https://genomic.social/@bioconductor/110537136393527330

📣#Bioconductor community! ⏰Deadline: this Wed May 31 23.59 ET🗓️

🎟Early reg & in-person scholarships #bioc2023: https://bioc2023.bioconductor.org/registration/

🏆BioC Award nominations: https://support.bioconductor.org/p/9152415/

🗳TAB nominations: https://support.bioconductor.org/p/9151209/

Don't miss these opportunities!🚀#Bioinformatics #Rstats

⏰3 days until the annual Smörgåsbord training course starts! There is still time to register if you want to participate #biocsmorgasbord

Join us for a week of free, online, self-paced #Bioconductor and #UseGalaxy #bioinformatics learning!

📅May 22-26
➡️https://gallantries.github.io/video-library/modules/bioconductor

Space, the current frontier. This is the second release of R pacakge Voyager. https://lambdamoses.github.io/thevoyages/posts/2023-04-26-voyager-1-2-0/

@bioconductor #Bioconductor #rstats

CSAMA 2023 - summer school in biological data science with #rstats and #Bioconductor

When? 11 - 16 June 2023
Where? Bressanone-Brixen, Italy

More details: https://csama2023.bioconductor.eu/

CSAMA 2023 - summer school in biological data science with #rstats and #Bioconductor

When? 11 - 16 June 2023
Where? Bressanone-Brixen, Italy

More details: https://csama2023.bioconductor.eu/

📢

Reminder for #Bioconductor and #genomics #rstats :rstats: users and developers:

The abstract submission deadline for the EuroBioc2023 conference closes on Monday 24 April, 5 pm (CEST).

https://eurobioc2023.bioconductor.org/

This year, it'll be organised in the beautiful city of Ghent, in Belgium

Send your abstracts

https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/Conference

📢

Reminder for #Bioconductor and #genomics #rstats :rstats: users and developers:

The abstract submission deadline for the EuroBioc2023 conference closes on Monday 24 April, 5 pm (CEST).

https://eurobioc2023.bioconductor.org/

This year, it'll be organised in the beautiful city of Ghent, in Belgium

Send your abstracts

https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/Conference

🌟#JobAlert: #Bioconductor 🧬is hiring a Cloud/DevOps Engineer!

Passionate about #opensource & have AWS experience? Apply now!

➡️ https://careers-dfci.icims.com/jobs/33592/cloud-devops-engineer%2c-bioconductor/job?mobile=false&width=888&height=500&bga=true&needsRedirect=false&jan1offset=0&jun1offset=60

Please boost to help spread the word! 🙏

#DevOps #CloudJobs #Bioinformatics #rstats

What should I name a function for returning a Seurat object?

In favour of snake_case, we have the tidyverse style guide (https://style.tidyverse.org/syntax.html#object-names), especially since tidyverse principles and dependencies are used in the package where this function lives.

In favour of camlelCase, we have BioConductor style (https://contributions.bioconductor.org/r-code.html#rcode-function-names), and this package will be submitted to BioConductor. Also there is the fact that Seurat styles itself in upper case.

#RStats #bioconductor #tidyverse

Upcoming feature in the next version of Voyager, for the Bioconductor 3.17 release: https://lambdamoses.github.io/thevoyages/posts/2023-03-25-multispati-part-2/ #spatial #bioconductor #rstats

@hadleywickham @haraldkliems

Thanks! I only have a package on #Bioconductor, they have a different standard.

A great write up of #cran and #Bioconductor dependencies.

https://chainsawriot.com/postmannheim/2023/02/26/rang.html

This project has been a fun introduction to the single cell world for me! I worked with Stefano to develop the package and the data hosting.

In the end, DuckDB was the silver bullet in making this work. Please give it a try and share your feedback!

#Bioconductor #SingleCell #RStats #Bioinformatics #DuckDB