Integrated Single-cell Navigation Portal (ISNAP)


ISNAP is a modular bioinformatics platform for publishing biological data that is compatible with numerous -omics workflows


What is the purpose of ISNAP?

  • Improve readership and increase credibility for research publications
  • Present and publish biological data in an organized and interactive layout
  • Abridge the gap between biology and data science
  • Open source scripts for reference

    • ISNAP-compatible workflows:

    Seurat: Single-cell and Spatial RNA-seq Data Exploration

    Seurat is a tool designed for QC, analysis, and exploration of single-cell and spatial RNA-seq data. Seurat enables users to interpret sources of cellular heterogeneity, identify differentially expressed genes, and integrate diverse types of -omics data.
    Publication:
    Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021)

    SCENIC: Infer Regulatory Networks from transcriptomic Data

    SCENIC is a tool for reconstructing gene regulatory networks across cell states. The inference is based on the co-expression between transcription factors and downstream target genes and their binding motifs.

    Publication:
    Aibar et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods (2017)

    RNA Velocity: Cell Trajectory Inference


    RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. This workflow utilizes scVelo and Velocyto to make observations and predictions about the future trajectory of cells.

    Publications:
    Bergen et al. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotech (2020)
    La Manno el al. RNA velocity of single cells. Nature (2018)

    Bulk RNA-seq: Differential Gene Expression Analysis


    RNA-seq analysis compares the transcriptome profiles across samples of interest through generalized linear modeling. We use a combination of tools including DESeq2 and EdgeR and their prescribed workflows for analysis.

    Publications:
    Love et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology (2014)
    Robinson el al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2010)



    Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction

    Tung et al., Nature Communications (2023)

    View Data on ISNAP | View Publication

    DPPIV+ fibro-adipogenic progenitors form the niche of adult skeletal muscle self-renewing resident macrophages

    Babaeijandaghi et al., Nature Communications (2023)

    View Data on ISNAP | View Publication

    Metabolic reprogramming of skeletal muscle by resident macrophages points to CSF1R inhibitors as muscular dystrophy therapeutics

    Babaeijandaghi et al., Science Translational Medicine (2023)

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    Activation of β-catenin in mesenchymal progenitors leads to muscle mass loss

    Kajabadi et al., Developmental Cell (2023)

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    TNFα and IFNγ cooperate for efficient pro- to anti-inflammatory transition of macrophages during muscle regeneration

    Babaeijandaghi et al., PNAS (2022)

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    Elevated numbers of infiltrating eosinophils accelerate the progression of Duchenne muscular dystrophy pathology in mdx mice

    Theret et al., Development (2022)

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    Brain pericytes and perivascular fibroblasts are stromal progenitors with dual functions in cerebrovascular regeneration after stroke

    Bernier et al., XXX (2024)

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    Stromal niche inflammation mediated by IL-1 signalling is a targetable driver of haematopoietic ageing

    Mitchell et al., Nature Cell Biology (2023)

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    Spatiotemporal mapping of immune and stem cell dysregulation after volumetric muscle loss

    Larouche et al., JCI Insight (2023)

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    Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells

    Yang et al., Cell Metabolism (2022)

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    Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration

    McKellar et al., Communications Biology (2021)

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    Cancer cell plasticity and MHC-II–mediated immune tolerance promote breast cancer metastasis to lymph nodes

    Lei et al., Journal of Experimental Medicine (2023)

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