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
If your tool doesn’t do this, but is useful for analysing single cell data we also accept light wrappers for some tools in
Interactive manifold viewers.
scVelo Helmholtz Munich
Spatial Transcriptomics Tools
squidpy Helmholtz Munich
Squidpy is a comprehensive toolkit for working with spatial single cell omics data.
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.
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.
Swan UC Irvine
Swan is a Python library designed for the analysis and visualization of transcriptomes, especially with long-read transcriptomes in mind. Users can add transcriptomes from different datasets and explore distinct splicing and expression patterns across datasets.
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.
CellRank Helmholtz Munich
CellRank is a framework to uncover cellular dynamics based on single-cell data. It incorporates modalities such as RNA velocity, pseudotime, developmental potential, real-time information, etc.
diffxpy Helmholtz Munich
Annotation/ Enrichment Analysis
Analyses using curated prior knowledge
decoupler is a collection of footprint enrichment methods that allows to infer transcription factor or 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.