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@EngreitzLab

Engreitz Lab

Engreitz Lab @ Stanford University

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  1. ABC-GWAS-Paper ABC-GWAS-Paper Public

    Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021

    PostScript 18 2

  2. CRISPRDesigner CRISPRDesigner Public

    Design and selection of gRNAs for pooled CRISPRi tiling screens

    Python 5 1

Repositories

Showing 10 of 47 repositories
  • scE2G Public

    Pipeline to run scE2G

    EngreitzLab/scE2G's past year of commit activity
    Python 68 MIT 8 6 3 Updated Oct 27, 2026
  • PerturbNMF Public

    Computaional pipeline for single-cell perturbation data

    EngreitzLab/PerturbNMF's past year of commit activity
    Python 10 MIT 3 0 3 Updated Oct 27, 2026
  • DC_TAP_Paper Public

    Workflow for analyzing DC TAP datasets

    EngreitzLab/DC_TAP_Paper's past year of commit activity
    HTML 0 MIT 2 0 2 Updated Oct 27, 2026
  • CRISPR_Pipeline Public Forked from pinellolab/CRISPR_Pipeline
    EngreitzLab/CRISPR_Pipeline's past year of commit activity
    Python 0 MIT 13 0 0 Updated Oct 26, 2026
  • broad-nnfc-cmo-multiome Public

    Reproducible analysis code for endothelial differentiation 10x Multiome CMO experiments across timepoints

    EngreitzLab/broad-nnfc-cmo-multiome's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 26, 2026
  • ipsc-ec-chrombpnet Public

    ChromBPNet pipeline for iPSC-to-EC differentiation: bias model training, contribution scores, motif discovery, and unified hit calling across 5 timepoints

    EngreitzLab/ipsc-ec-chrombpnet's past year of commit activity
    Python 0 0 0 0 Updated Oct 22, 2026
  • generate-principal-pseudobulks Public

    Select QC thresholds based on per-cell quality reports and QC filter + merge ATAC fragment files & RNA count matrices

    EngreitzLab/generate-principal-pseudobulks's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 21, 2026
  • crispr-analysis-utils Public

    Utilities and reusable scripts for CRISPR screen analysis, preprocessing, and downstream workflows.

    EngreitzLab/crispr-analysis-utils's past year of commit activity
    Python 1 MIT 0 0 0 Updated Oct 15, 2026
  • sk_cNMF Public Forked from dylkot/cNMF

    Modified sklearn based cNMF

    EngreitzLab/sk_cNMF's past year of commit activity
    Jupyter Notebook 0 MIT 78 0 0 Updated Oct 13, 2026
  • Swap-seq Public

    Analysis for Swap-seq experiments

    EngreitzLab/Swap-seq's past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Oct 5, 2026
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