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@shendurelab

Jay Shendure's lab at the University of Washington

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  1. LACHESIS LACHESIS Public

    The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

    C++ 80 30

  2. cfDNA cfDNA Public

    Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA

    Python 78 32

  3. MPRAflow MPRAflow Public

    A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

    Python 35 16

  4. mouse-atac mouse-atac Public

    Repo for website and other code for mouse sci-ATAC-seq project

    Python 29 29

  5. single-cell-ko-screens single-cell-ko-screens Public

    Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hill, McFaline-Figueroa et al.

    R 26 11

  6. MIPGEN MIPGEN Public

    One stop MIP design and analysis

    C++ 24 20

Repositories

Showing 10 of 31 repositories
  • EBTF Public
    shendurelab/EBTF’s past year of commit activity
    R 0 0 0 0 Updated Feb 11, 2026
  • Neural_CRE_MPRA_CRISPRa Public

    Analysis and visualization code for "Large-scale discovery of neural enhancers for cis-regulation therapies"

    shendurelab/Neural_CRE_MPRA_CRISPRa’s past year of commit activity
    R 0 0 0 0 Updated Oct 24, 2025
  • ENGRAM Public
    shendurelab/ENGRAM’s past year of commit activity
    Jupyter Notebook 3 MIT 0 0 0 Updated Oct 19, 2025
  • AP_human_gastruloids Public

    Scripts for data processing and analysis used in the manuscript 'Dual-patterned Pluripotent Stem Cells Self-Organize into a Human Embryo Model with Extended Anterior-Posterior Patterning.'

    shendurelab/AP_human_gastruloids’s past year of commit activity
    R 0 0 0 0 Updated Sep 17, 2025
  • Lindel Public
    shendurelab/Lindel’s past year of commit activity
    Python 5 MIT 10 3 0 Updated Jul 17, 2025
  • Prime-del Public
    shendurelab/Prime-del’s past year of commit activity
    Python 3 MIT 0 0 0 Updated Jul 17, 2025
  • Diversified_Parts Public

    Analysis and visualization code for "Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording"

    shendurelab/Diversified_Parts’s past year of commit activity
    Python 0 0 0 0 Updated Jul 10, 2025
  • DTT Public

    The scripts used for the clonal gastruloid lineage tracing project.

    shendurelab/DTT’s past year of commit activity
    R 1 0 0 0 Updated Jun 8, 2025
  • scQers Public

    Scripts, plasmid maps, and amplicon maps for: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

    shendurelab/scQers’s past year of commit activity
    R 3 MIT 1 0 1 Updated Jan 20, 2025
  • MPRAflow Public

    A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

    shendurelab/MPRAflow’s past year of commit activity
    Python 35 Apache-2.0 16 13 2 Updated Jan 6, 2025
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