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@JEFworks-Lab

JEFworks Lab

JEFworks Lab at Johns Hopkins University

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  1. STdeconvolveSTdeconvolvePublic

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

    R 151 18

  2. STalignSTalignPublic

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

    HTML 92 23

  3. CRAWDADCRAWDADPublic

    Cell-type Relationship Analysis Workflow Done Across Distances

    R 38 6

  4. velovizvelovizPublic

    RNA-velocity informed embeddings for visualizing cellular trajectories

    R 44 3

  5. MERINGUEMERINGUEPublic

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

    R 81 6

  6. HoneyBADGERHoneyBADGERPublic

    HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

    R 99 31

Repositories

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Showing 10 of 22 repositories
  • off-target-probe-tracker Public

    Pipeline to predict off-target binding via probe sequences

    JEFworks-Lab/off-target-probe-tracker’s past year of commit activity
    Python 13GPL-3.0 2 3 0 UpdatedDec 16, 2025
  • 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 50 0 0 UpdatedDec 15, 2025
  • STARIT Public

    Spatial Transcriptomics As Rasterized Tensors (STARIT)

    JEFworks-Lab/STARIT’s past year of commit activity
    Jupyter Notebook 1GPL-3.00 0 0 UpdatedDec 10, 2025
  • CRAWDAD Public

    Cell-type Relationship Analysis Workflow Done Across Distances

    JEFworks-Lab/CRAWDAD’s past year of commit activity
    R 38GPL-3.0 6 4 0 UpdatedNov 18, 2025
  • JEFworks-Lab/jefworks-lab.github.io’s past year of commit activity
    Jupyter Notebook 4CC-BY-4.0 30 1 0 UpdatedOct 20, 2025
  • STdeconvolve Public

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

    JEFworks-Lab/STdeconvolve’s past year of commit activity
    R 151 18 20 0 UpdatedAug 3, 2025
  • JEFworks-Lab/vitessce-cold-ischemia’s past year of commit activity
    JavaScript00 0 0 UpdatedMay 30, 2025
  • 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 19 5 1 0 UpdatedApr 23, 2025
  • JEFworks-Lab/genomic-data-visualization-2025’s past year of commit activity
    JavaScript0 29 0 0 UpdatedMar 14, 2025
  • scatterbar Public

    Scatterbar - data visualization for proportional data across many spatially resolved coordinates

    JEFworks-Lab/scatterbar’s past year of commit activity
    R 11GPL-3.0 1 1 0 UpdatedMar 3, 2025

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