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@shendurelab Jay Shendure's lab at the University of Washington

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    31 repositories

    • hub

      Public
      0•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • Prime-del

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Mar 7, 2026Mar 7, 2026

    • Lindel

      Public
      Python
      •
      MIT License
      •10•5•3•0•Updated Mar 7, 2026Mar 7, 2026

    • EBTF

      Public
      R
      •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • Neural_CRE_MPRA_CRISPRa

      Public
      Analysis and visualization code for "Large-scale discovery of neural enhancers for cis-regulation therapies"
      R
      •0•0•0•0•Updated Oct 24, 2025Oct 24, 2025

    • ENGRAM

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Oct 19, 2025Oct 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 Ant…
      R
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • Diversified_Parts

      Public
      Analysis and visualization code for "Diversified, miniaturized and ancestral parts for mammalian genome engineering and molecular recording"
      Python
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • DTT

      Public
      The scripts used for the clonal gastruloid lineage tracing project.
      R
      •0•1•0•0•Updated Jun 8, 2025Jun 8, 2025

    • scQers

      Public
      Scripts, plasmid maps, and amplicon maps for: Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
      R
      •
      MIT License
      •1•3•0•1•Updated Jan 20, 2025Jan 20, 2025

    • MPRAflow

      Public
      A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data
      Python
      •
      Apache License 2.0
      •17•35•13•2•Updated Jan 6, 2025Jan 6, 2025

    • multiplex_scCRISPRa_screening

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 24, 2024Oct 24, 2024

    • Human-RA-Gastruloid

      Public
      Code relevant for analysis of human RA gastruloids
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jun 18, 2024Jun 18, 2024

    • MMCA

      Public
      The scripts used for performing data analysis in the MMCA project
      R
      •
      MIT License
      •0•5•1•0•Updated Jun 12, 2024Jun 12, 2024

    • ptolemy-ui

      Public
      Vue
      •0•0•0•0•Updated Jul 20, 2022Jul 20, 2022

    • ptolemy-api

      Public
      Python
      •0•0•0•0•Updated Jul 20, 2022Jul 20, 2022

    • DNATickerTape

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 4, 2022Jul 4, 2022

    • mmca-website

      Public
      Interactive 3D visualization for mouse mutant cell x gene data
      JavaScript
      •1•1•0•0•Updated Apr 25, 2022Apr 25, 2022

    • 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 e…
      R
      •11•26•6•0•Updated Jan 25, 2022Jan 25, 2022

    • AssemblyByPacBio

      Public
      Scripts to assign a barcode to a variable region from PacBio SMRT reads
      Python
      •3•6•0•0•Updated Nov 18, 2021Nov 18, 2021

    • human-atac

      Public
      Code for demultiplexing and cell barcode assignment for sci-ATAC3 runs
      Python
      •
      MIT License
      •1•5•0•0•Updated Apr 20, 2021Apr 20, 2021

    • mouse-atac

      Public
      Repo for website and other code for mouse sci-ATAC-seq project
      Python
      •29•29•5•0•Updated Oct 1, 2020Oct 1, 2020

    • MIPGEN

      Public
      One stop MIP design and analysis
      C++
      •
      Other
      •21•24•4•1•Updated Sep 30, 2020Sep 30, 2020

    • tafka-crisprQTL

      Public
      Code associated with tafka-crisprQTL (Gasperini, et al. 2019)
      R
      •1•3•1•0•Updated Jul 27, 2020Jul 27, 2020

    • cfDNA

      Public
      Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA
      Python
      •
      MIT License
      •32•78•2•0•Updated Jul 22, 2020Jul 22, 2020

    • fly-atac

      Public
      Code relevant to sci-ATAC-seq of Drosophila embryogenesis.
      Python
      •
      MIT License
      •8•22•1•0•Updated Jun 9, 2019Jun 9, 2019

    • MAP-C

      Public
      Code and annotation files for MAP-C paper
      HTML
      •
      MIT License
      •1•0•0•0•Updated May 16, 2019May 16, 2019

    • MetaPhase

      Public
      The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)
      C++
      •7•17•2•1•Updated Oct 12, 2018Oct 12, 2018

    • LACHESIS

      Public
      The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
      C++
      •
      Other
      •30•80•46•2•Updated Oct 12, 2018Oct 12, 2018

    • saturationGenomeEditing_pipeline

      Public
      Python
      •6•5•0•0•Updated Jul 10, 2018Jul 10, 2018
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