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.
CellRank Helmholtz MunichCellRank 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.
scvi-tools Berkeleyscvi-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 Innsbruckscirpy is a scanpy extension to expore single-cell T-cell receptor (TCR) and B-cell receptor (BCR) repertoires.
dandelion University of Cambridgedandelion is a single-cell BCR-seq network analysis package that integrates with transcriptomic data analyzed via scanpy.
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 UniversityIntuitive Nonparametric Gene Network Search Algorithm that learns from existing biological pathways & multiplicative gene interference patterns.