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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 178 51

  2. CRISPResso2 CRISPResso2 Public

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

    Python 331 111

  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 26 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
  • 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 331 111 50 (1 issue needs help) 3 Updated Jan 20, 2026
  • PerTurbo Public

    Robust and efficient analysis of single-cell perturbation studies

    pinellolab/PerTurbo’s past year of commit activity
    Python 12 MIT 2 1 2 Updated Jan 20, 2026
  • CRISPR-HAWK Public

    Variant- and Haplotype-aware CRISPR guide design toolkit

    pinellolab/CRISPR-HAWK’s past year of commit activity
    Python 5 3 0 0 Updated Jan 19, 2026
  • EPInformer Public

    code to run EPInformer for gene expression prediction and gene-enhancer link prediction

    pinellolab/EPInformer’s past year of commit activity
    Jupyter Notebook 44 MIT 10 0 1 Updated Jan 19, 2026
  • CRISPRme Public

    Variant-aware CRISPR off-target nomination

    pinellolab/CRISPRme’s past year of commit activity
    Python 24 9 1 0 Updated Jan 16, 2026
  • CRISPR_Pipeline Public
    pinellolab/CRISPR_Pipeline’s past year of commit activity
    Python 13 MIT 6 7 2 Updated Jan 14, 2026
  • SVG_Benchmarking Public

    Benchmarking methods for identification of spatially variable genes

    pinellolab/SVG_Benchmarking’s past year of commit activity
    Jupyter Notebook 7 MIT 2 5 1 Updated Jan 9, 2026
  • 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 Jan 8, 2026
  • CRISPR-Correct Public

    Perform CRISPR guide mapping and analysis that considers protospace self-editing and surrogate sensor sequences. Self-editing aware mapping takes a hamming-distance approach unbiased by expectations in editing patterns.

    pinellolab/CRISPR-Correct’s past year of commit activity
    Python 4 AGPL-3.0 0 3 0 Updated Jan 8, 2026
  • ACCESS-ATAC Public
    pinellolab/ACCESS-ATAC’s past year of commit activity
    Python 0 0 0 0 Updated Jan 6, 2026
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