Ecosystem

Note

If you’d like to see your tool included here, please open a pull request!

With ecosystem, we mean the broader single-cell related tools that operate on AnnData. If your tool doesn’t do this, but is useful for analysing single cell data we also accept light wrappers for some tools in scanpy.external.

Viewers

Interactive manifold viewers.

cellxgene via direct reading of .h5ad CZI
cirrocumulus via direct reading of .h5ad Broad Inst.
cell browser via exporing through cellbrowser() UCSC
SPRING via exporting through spring_project() Harvard Med

Portals

the Gene Expression Analysis Resource U Maryland
the Galaxy Project for the Human Cell Atlas [tweet] U Freiburg
the Expression Atlas EMBL-EBI

RNA velocity

scVelo Helmholtz Munich

Fate mapping

CellRank Helmholtz Munich

CellRank is a toolkit to uncover cellular dynamics based on scRNA-seq data with RNA velocity annotation by detecting initial and terminal populations, inferring fate potentials and uncovering gene expression trends towards specific terminal populations.

Differential expression

diffxpy Helmholtz Munich

Data integration

scanaroma MIT

Modeling perturbations

scGen / trVAE Helmholtz Munich

scvi-tools

scvi-tools Berkeley

scvi-tools hosts deep generative models (DGM) for end-to-end analysis of single-cell omics data (e.g., scVI, scANVI, totalVI). It also contains several primitives to build novel DGMs.

Adaptive immune receptor repertoire (AIRR)

scirpy Medical University of Innsbruck

scirpy is a scanpy extension to expore single-cell T-cell receptor (TCR) and B-cell receptor (BCR) repertoires.
dandelion University of Cambridge

dandelion is a single-cell BCR-seq network analysis package that integrates with transcriptomic data analyzed via scanpy.

Feature selection

triku 🦔 Biodonostia Health Research Institute

Annotation/ Enrichment Analysis

Analyses using curated prior knowledge

dorothea for Transcription Factor activities Institute for Computational Biomedicine, Heidelberg University
progeny for footprint-based pathway activities Institute for Computational Biomedicine, Heidelberg University
Cubé Harvard University

Intuitive Nonparametric Gene Network Search Algorithm that learns from existing biological pathways & multiplicative gene interference patterns.

Spatial Transcriptomics Tools

PASTE Princeton

PASTE is a computational method to align and integrate spatial transcriptomics data across adjacent tissue slices by leveraging both gene expression similarity and spatial distances between spots.