scverse

AnnData object creation, manipulation, and visualization for single-cell RNA-seq data analysis

End-to-end scRNA-seq analysis of 10x Genomics PBMC 3k using Scanpy; QC, clustering, manual and automated cell-type annotation

Single-cell mass spectrometry quantification (DIA-NN pg_matrix, long tables) to AnnData/MuData with MS-aware QC.

Validate the semantic correctness, metadata completeness, provenance and AI readiness of Cell Painting datasets represented in AnnData.

scverse AnnData tutorial implementation

Muon website

Explicit MAD-based QC flagging and robust scaling for Python, AnnData, and scverse workflows.

Validate and package reproducible computational biology analysis runs using RO-Crate.

Structure and process genomic, transcriptomic, and machine learning data with this compact Python framework.

Single-cell alternative-splicing analysis

Website of scVI-Tools: Deep probabilistic analysis of single-cell and spatial omics data

Ublind challenges the ways we interact with high dimensional data and overcomes a fundamental limitation in accessibility of latent representations of data

Dimensionality reduction and interactive web visualization for the scverse 2024 conference

Tutorials and helpers for downstream analysis of Cell Painting data with scverse tools (anndata, scanpy, decoupler, pertpy, squidpy, rapids-singlecell)

Joint MS-proteomics analysis with Python and R packages

Regularized scVI for complex multiome single-cell/nucleus datasets: ambient RNA correction, dispersion prior, and batch-free decoder act as structural inductive biases that make large-architecture VAEs well-behaved without per-dataset tuning.

Unified open-source motorsport AI ecosystem: shared ML & data infrastructure (motorsport-core, motorsport-data) powering per-series prediction projects (RaceIQ F1, F2, and more) with a central project catalog. scverse-style.

CloneTrast reveals pan-cancer clonal niches of T-cells from single-cell RNA sequencing using contrastive learning

A high-performance Python package for single-cell genomics

Lightweight helper to install scvi-tools in Google Colab