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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 319 107

  3. haystack_bio haystack_bio Public

    Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

    HTML 47 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 2

Repositories

Showing 10 of 64 repositories
  • cell2net Public

    Mapping multi-scale and genotype-specific gene regualtion

    pinellolab/cell2net’s past year of commit activity
    Jupyter Notebook 0 MIT 0 1 0 Updated Oct 17, 2025
  • pyrovelocity Public

    𝒫robabilistic modeling of RNA velocity ⬱

    pinellolab/pyrovelocity’s past year of commit activity
    Python 49 AGPL-3.0 5 11 17 Updated Oct 16, 2025
  • CRISPR_Pipeline Public
    pinellolab/CRISPR_Pipeline’s past year of commit activity
    Python 13 MIT 5 7 0 Updated Oct 15, 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 319 107 42 (1 issue needs help) 4 Updated Oct 14, 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 Oct 14, 2025
  • CRISPR-millipede-helper Public

    Helper utility function for running CRISPR-millipede pipelines

    pinellolab/CRISPR-millipede-helper’s past year of commit activity
    Python 0 0 0 0 Updated Oct 9, 2025
  • dictys Public

    Context specific and dynamic gene regulatory network reconstruction and analysis

    pinellolab/dictys’s past year of commit activity
    Python 122 AGPL-3.0 15 0 0 Updated Oct 8, 2025
  • DNA-Diffusion Public

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

    pinellolab/DNA-Diffusion’s past year of commit activity
    Python 413 53 2 5 Updated Oct 8, 2025
  • CRISPRme Public
    pinellolab/CRISPRme’s past year of commit activity
    Python 22 9 1 1 Updated Oct 6, 2025
  • PerTurbo Public

    Robust and efficient analysis of single-cell perturbation studies

    pinellolab/PerTurbo’s past year of commit activity
    Python 3 MIT 0 1 0 Updated Oct 1, 2025
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