The new `rds2py` release brings R's native serialization to Python. Now you can write complex BiocPy objects like SummarizedExperiment, SingleCellExperiment, and GenomicRanges as RDS files. They’ll open in R seamlessly with no extra steps: ``` import rds2py rds2py.write_rds(my_obj, "data.rds") ```

chronometre: A new package (pair) demo for R and Python Efficient yet simple object exchange between R and Python dirk.eddelbuettel.com/blog/2026/02... #rstats #rcpp #python #datascience

A follow up, you can fetch Organism DB objects straight from AnnotationHub! The `orgdb` Python package makes querying annotations efficient and easy. repo: github.com/BiocPy/orgdb #biocpy #orgdb

Jayaram Kancherla@jkanche.bsky.social · 8mo ago

Seamlessly access R/Bioconductor annotations in Python! The new "txdb" package lets you load standard TxDb SQLite databases and work with genomic features as native #BiocPy `GenomicRanges` objects. Try it: `pip install txdb` docs: github.com/BiocPy/txdb

Seamlessly access R/Bioconductor annotations in Python! The new "txdb" package lets you load standard TxDb SQLite databases and work with genomic features as native #BiocPy `GenomicRanges` objects. Try it: `pip install txdb` docs: github.com/BiocPy/txdb

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

nature.com

It's official! The #tidyomics blog is up! 🚀 Here, the introductory post tidyomics.github.io/tidyomicsBlo... This blog aims to publish not only news about our community but also anything related to tidy interfaces, opinions, events, and more. Plz share! 🙏 @bioconductor.bsky.social #rstats

The Tidyomics Ecosystem – tidyomicsBlog

An introduction to the tidyomics ecosystem, including principles, core packages, publications, and community resources for tidy omic analysis.

tidyomics.github.io

The GenomicRanges (github.com/BiocPy/GenomicRanges) package for Python got a major speed boost (v0.7.0+) thanks to Aaron’s blazing-fast C++ nclist interval indexing! #Bioinformatics #Genomics #Bioconductor

GitHub - BiocPy/GenomicRanges: Container class to represent genomic locations and support genomic analysis

Container class to represent genomic locations and support genomic analysis - BiocPy/GenomicRanges

github.com

Hey #genomics, #bioinformatics & #algorithms peeps 💻🧬. If you haven't seen the CfP for WABI '25 yet, check out the website wabiconf.github.io/2025/. It will be held at UMD @umdscience.bsky.social with Broňa Brejová & myself as co-chairs! Submit your exciting & late-breaking algorithmic work to WABI

If this generation is Gen Alpha, I say we call the next one Gen AI—because they'll probably ask ChatGPT than reddit for advice.

In addition, ArtifactDB (github.com/ArtifactDB) provides language agnostic representations to save and load Bioconductor objects.

ArtifactDB

Metadata and file store for arbitrary data objects - ArtifactDB

github.com

Malte Kuehl@maltekuehl.com · 2y ago

This package is helpful, however, I have encountered cases in which it does not work. Also unsure whether yet another file format will help the ecosystem standardize. My hope are AnnDataR & readRDS (BiocPy) together with wrappers to map between the formats in each ecosystem, no intermediaries

Hello world!