diff --git a/content/blog/2025-core-expansion.md b/content/blog/2025-core-expansion.md new file mode 100644 index 0000000..3683e33 --- /dev/null +++ b/content/blog/2025-core-expansion.md @@ -0,0 +1,81 @@ ++++ +title = "Four new scverse core packages" +date = 2025-07-01T00:00:05+01:00 +description = "scverse expands with new core packages." +author = "Lukas Heumos" +draft = false ++++ + +# Four new core packages in scverse + +We're happy to announce that four new packages have joined the scverse core ecosystem: [SnapATAC2](https://github.com/scverse/snapatac2), [rapids-singlecell](https://github.com/scverse/rapids_singlecell), [pertpy](https://github.com/scverse/pertpy), and [decoupler](https://github.com/scverse/decoupler). +This broadens the scope of scverse beyond our so far supported modalities and brings in new functionality for epigenomics, perturbation screens, GPU acceleration, and functional inference. + +Single-cell analysis is evolving rapidly, with new experimental modalities and larger datasets becoming the norm. +To keep up with this, we’re expanding scverse to support more domains, more data types, and more scalable computing backends. +By bringing these mature, well-maintained tools into the core, we aim to provide a consistent and interoperable foundation across all stages of single-cell analysis. + +We're also welcoming the following lead maintainers to the scverse core developer team: +- **Kai Zhang** for **snapatac2** +- **Pau Badia i Mompel** for **decoupler** + +## SnapATAC2 + +[SnapATAC2](https://github.com/scverse/snapatac2) enables fast, scalable analysis of single-cell ATAC-seq and related epigenomic data. +Built in Rust with a Python front end, it handles millions of cells efficiently. +The package offers preprocessing, dimensionality reduction, clustering, and visualization methods. +All outputs are stored in AnnData and integrate seamlessly with scanpy and other scverse frameworks. + +SnapATAC2 overview + +## rapids-singlecell + +[rapids-singlecell](https://github.com/scverse/rapids_singlecell) accelerates the full single-cell analysis pipeline through GPU acceleration with CuPy and NVIDIA RAPIDS. +Core steps—including PCA, neighborhood graph construction, and clustering—are executed on GPU using cuML, cuGraph, and custom CUDA/CuPy kernels for peak performance. + +RSC integrates directly with AnnData and offers near drop-in replacements not only for scanpy, but also for selected functions from decoupler and squidpy. +By preserving familiar APIs and data structures, it enables seamless GPU acceleration of existing workflows—scaling to millions of cells without the computational bottlenecks of CPU-based analysis. + +RSC overview + +For more details, we refer to a recent blog post by NVIDIA: [Driving Toward Billion-Cell Analysis and Biological Breakthroughs with RAPIDS-singlecell](https://developer.nvidia.com/blog/driving-toward-billion-cell-analysis-and-biological-breakthroughs-with-rapids-singlecell) + +## pertpy + +[pertpy](https://github.com/scverse/pertpy) focuses on single-cell perturbation screens, including CRISPR and compound treatments. +It supports differential analysis, signature scoring, and dose-response modeling. +Metadata handling and visualization are tailored for perturbation-specific use cases. +Built on AnnData and scverse libraries, pertpy fits smoothly into existing pipelines. + +pertpy overview + +## decoupler + +[decoupler](https://github.com/scverse/decoupler) enables the inference of enrichment scores from omics data using prior knowledge. +It maps omics profiles to annotated biological sets, such as transcription factors, pathways, or kinases, using methods like GSEA, GSVA, and linear models. +Designed for bulk, single-cell and spatial data, decoupler works directly with our scverse core data structures. + +decoupler overview + +## What this means + +We're continuing to support a modular but coherent ecosystem where high-quality tools can interoperate. +These additions bring coverage of new data types and analysis goals while staying within the same technical foundations. +All packages use our scverse core data structures, follow shared conventions, and benefit from a growing set of shared infrastructure and community practices. +We aim to keep development decentralized and open while improving alignment across projects. + +## Get involved + +If you're building something new, we'd love to have your work be a part of the [scverse ecosystem](https://github.com/scverse/ecosystem-packages). +If you're our tools, please share feedback or ideas via the respective issue trackers. +The best places to start are [scverse.org](https://scverse.org), [github.com/scverse](https://github.com/scverse), and our [scverse zulip chat](https://scverse.zulipchat.com/). +We're always looking for more contributors to our packages but especially also for community related work. +Please reach out! + +## Thank you + +We’re grateful to the maintainers of these packages for their work and commitment to open, reusable tools. +Their contributions help make the scverse ecosystem more useful, inclusive, and sustainable. +We’re also thankful to the community for using, testing, and contributing to these tools — your feedback drives everything we do. + +*— The scverse core team* diff --git a/static/img/blog/decoupler_overview.png b/static/img/blog/decoupler_overview.png new file mode 100644 index 0000000..d785348 Binary files /dev/null and b/static/img/blog/decoupler_overview.png differ diff --git a/static/img/blog/rsc_overview.png b/static/img/blog/rsc_overview.png new file mode 100644 index 0000000..c6d46af Binary files /dev/null and b/static/img/blog/rsc_overview.png differ diff --git a/static/img/blog/snapatac2_overview.png b/static/img/blog/snapatac2_overview.png new file mode 100644 index 0000000..5a271d9 Binary files /dev/null and b/static/img/blog/snapatac2_overview.png differ