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

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

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

Chromatin analysis module

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

Python port of R limma for differential expression analysis

Dimensionality reduction and interactive web visualization for the scverse 2024 conference

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

scverse AnnData tutorial implementation

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

A Python package for unsupervised analysis of spatial (prote)omics data.

A high-performance Python package for single-cell genomics

Muon website

Governance docs for scverse

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

A unified evaluation framework for single-cell perturbation prediction

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

A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.