Ecosystem

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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

• vitessce for purely browser based viewing of zarr formatted AnnData files 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

Modalities

RNA velocity

• scVelo Helmholtz Munich

Spatial Transcriptomics Tools

• squidpy Helmholtz Munich

  Squidpy is a comprehensive toolkit for working with spatial single cell omics data.

• 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.

• bento 🍱 UC San Diego

  Bento is an accessible Python toolkit for performing subcellular analysis of spatial transcriptomics data.

Multimodal integration

• MUON and MuData EMBL/ DKFZ

  MUON, and it’s associated data structure MuData are designed to organise, analyse, visualise, and exchange multimodal data. MUON enables a range of analyses for ATAC and CITE-seq, from data preprocessing to flexible multi-omics alignment.

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.

Long reads

• 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.

Analysis methods

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.

Fate mapping

• 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.

Differential expression

• diffxpy Helmholtz Munich

Data integration

• scanaroma MIT

Modeling perturbations

• scGen / trVAE Helmholtz Munich

Feature selection

• triku 🦔 Biodonostia Health Research Institute

• CIARA Helmholtz Munich

  CIARA is an algorithm for feature selection, that aims for the identification of rare cell types via scRNA-Seq data in scanpy.

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.