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@pinellolab

Pinello Lab

Massachusetts General Hospital/Harvard Medical School

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  1. STREAM STREAM Public

    STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

    Jupyter Notebook 177 51

  2. CRISPResso2 CRISPResso2 Public

    Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

    Python 329 110

  3. haystack_bio haystack_bio Public

    Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

    HTML 46 11

  4. CRISPR-SURF CRISPR-SURF Public

    Python 17 3

  5. PrimeDesign PrimeDesign Public

    Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!

    Python 25 6

  6. MotifRaptor MotifRaptor Public

    Explore the effect of genetic variants on transcription factor binding sites

    Python 8 3

Repositories

Showing 10 of 66 repositories
  • DNA-Diffusion Public

    🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

    pinellolab/DNA-Diffusion’s past year of commit activity
    Python 422 54 1 1 Updated Dec 22, 2025
  • CRISPResso2 Public

    Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

    pinellolab/CRISPResso2’s past year of commit activity
    Python 329 110 50 (1 issue needs help) 6 Updated Dec 19, 2025
  • CRISPR-HAWK Public

    Variant- and Haplotype-aware CRISPR guide design toolkit

    pinellolab/CRISPR-HAWK’s past year of commit activity
    Python 1 1 0 0 Updated Dec 18, 2025
  • CRISPRme Public

    Variant-aware CRISPR off-target nomination

    pinellolab/CRISPRme’s past year of commit activity
    Python 23 9 1 0 Updated Dec 18, 2025
  • simba-plus Public

    SIMBA+

    pinellolab/simba-plus’s past year of commit activity
    Python 0 1 0 0 Updated Dec 17, 2025
  • CRISPR_Pipeline Public
    pinellolab/CRISPR_Pipeline’s past year of commit activity
    Python 13 MIT 6 7 1 Updated Dec 17, 2025
  • PerTurbo Public

    Robust and efficient analysis of single-cell perturbation studies

    pinellolab/PerTurbo’s past year of commit activity
    Python 12 MIT 1 1 1 Updated Dec 16, 2025
  • CRISPR-millipede-target Public

    Calculate the enrichment scores of CRISPR alleles and variants from direct target amplicon-sequencing data using Bayesian linear regression model "millipede".

    pinellolab/CRISPR-millipede-target’s past year of commit activity
    Jupyter Notebook 1 AGPL-3.0 0 1 1 Updated Dec 7, 2025
  • ACCESS-ATAC Public
    pinellolab/ACCESS-ATAC’s past year of commit activity
    Python 0 0 0 0 Updated Dec 5, 2025
  • cell2net Public

    Mapping multi-scale gene regualtion using single-cell multiome

    pinellolab/cell2net’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Nov 28, 2025
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