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  1. STREAM STREAM Public

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

    Jupyter Notebook 184 51

  2. CRISPResso2 CRISPResso2 Public

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

    Python 359 120

  3. haystack_bio haystack_bio Public

    Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

    HTML 49 12

  4. CRISPR-SURF CRISPR-SURF Public

    Python 20 4

  5. PrimeDesign PrimeDesign Public

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

    Python 32 10

  6. MotifRaptor MotifRaptor Public

    Explore the effect of genetic variants on transcription factor binding sites

    Python 9 4

Repositories

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Showing 10 of 71 repositories
  • CRISPRLungo Public

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    pinellolab/CRISPRLungo's past year of commit activity
    Python 13 4 0 0 Updated Nov 11, 2026
  • CRISPResso2 Public

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

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    pinellolab/CRISPResso2's past year of commit activity
    Python 359 120 49 (1 issue needs help) 2 Updated Nov 10, 2026
  • CRISPRitz Public

    Tool package to perform in-silico CRISPR analysis and assessment

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    pinellolab/CRISPRitz's past year of commit activity
    C++ 43 11 0 2 Updated Nov 10, 2026
  • crisprme-plus Public

    CRISPRme+ — web/data-manager + optimization successor lineage to CRISPRme

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    pinellolab/crisprme-plus's past year of commit activity
    Python 3 1 0 3 Updated Nov 5, 2026
  • DNA-Diffusion Public

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

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    pinellolab/DNA-Diffusion's past year of commit activity
    Python 491 63 1 6 Updated Oct 28, 2026
  • CRISPR_Pipeline Public

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    pinellolab/CRISPR_Pipeline's past year of commit activity
    Python 16 MIT 13 8 6 Updated Oct 28, 2026
  • PyroPPI Public

    Hierarchical Bayesian modelling of PPI Recorder screens

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    pinellolab/PyroPPI's past year of commit activity
    Jupyter Notebook 0 AGPL-3.0 0 0 0 Updated Oct 19, 2026
  • chorus Public

    One interface to nine genomic deep-learning oracles — variant effect prediction, calibrated per-track percentiles, and plain-English analysis through MCP.

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    pinellolab/chorus's past year of commit activity
    Python 72 MIT 14 0 1 Updated Oct 15, 2026
  • crisprme-skill Public

    Claude Code Agent Skill for running CRISPRme+ variant- and haplotype-aware CRISPR off-target searches from plain-language requests

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    pinellolab/crisprme-skill's past year of commit activity
    Python 0 0 0 0 Updated Oct 14, 2026
  • CRISPRme Public

    Variant-aware CRISPR off-target nomination

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    pinellolab/CRISPRme's past year of commit activity
    Python 28 10 2 3 Updated Oct 8, 2026
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