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@JEFworks-Lab

JEFworks Lab

JEFworks Lab at Johns Hopkins University

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  1. STdeconvolve STdeconvolve Public

    Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data

    R 161 21

  2. STalign STalign Public

    Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

    Python 116 27

  3. CRAWDAD CRAWDAD Public

    Cell-type Relationship Analysis Workflow Done Across Distances

    R 42 7

  4. SEraster SEraster Public

    Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis

    R 20 5

  5. STcompare STcompare Public

    STcompare is an R package for comparing spatial gene expression patterns across spatial transcriptomics (ST) datasets

    R 14 2

  6. STARIT STARIT Public

    Spatial Transcriptomics As Rasterized Tensors (STARIT)

    Jupyter Notebook 4

Repositories

Showing 10 of 30 repositories
  • jefworks-lab.github.io Public
    JEFworks-Lab/jefworks-lab.github.io's past year of commit activity
    Jupyter Notebook 4 CC-BY-4.0 32 1 0 Updated Oct 23, 2026
  • STcompare Public

    STcompare is an R package for comparing spatial gene expression patterns across spatial transcriptomics (ST) datasets

    JEFworks-Lab/STcompare's past year of commit activity
    R 14 2 2 0 Updated Oct 19, 2026
  • STalign Public

    Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

    JEFworks-Lab/STalign's past year of commit activity
    Python 116 GPL-3.0 27 21 2 Updated Oct 16, 2026
  • STARIT Public

    Spatial Transcriptomics As Rasterized Tensors (STARIT)

    JEFworks-Lab/STARIT's past year of commit activity
    Jupyter Notebook 4 GPL-3.0 0 0 0 Updated Oct 5, 2026
  • SG-Isoform-Explorer Public

    An interactive, isoform-aware RNA-seq browser for the stress-granule (SG) and Total RNA samples from Khong et al. 2017. The included dataset focuses on CAPNS1 and ANXA2, aligned to GRCh38 and annotated with Ensembl release 115.

    JEFworks-Lab/SG-Isoform-Explorer's past year of commit activity
    JavaScript 0 GPL-3.0 0 0 0 Updated Oct 5, 2026
  • SEraster Public

    Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis

    JEFworks-Lab/SEraster's past year of commit activity
    R 20 5 1 0 Updated Sep 29, 2026
  • CellCarto-3DEEP Public

    3DEEP Hair Follicle Data Explorer

    JEFworks-Lab/CellCarto-3DEEP's past year of commit activity
    JavaScript 0 1 0 0 Updated Jul 20, 2026
  • CellCarto-ColdIschemia Public
    JEFworks-Lab/CellCarto-ColdIschemia's past year of commit activity
    CSS 0 MIT 0 0 0 Updated Jul 10, 2026
  • MERINGUE Public

    characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

    JEFworks-Lab/MERINGUE's past year of commit activity
    R 102 GPL-3.0 7 8 0 Updated Apr 30, 2026
  • genomic-data-visualization-2026 Public
    JEFworks-Lab/genomic-data-visualization-2026's past year of commit activity
    JavaScript 0 28 0 0 Updated Apr 17, 2026
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