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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 321 108

  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 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 321 108 45 (1 issue needs help) 3 Updated Nov 10, 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 Nov 10, 2025
  • CRISPRme Public

    Variant-aware CRISPR off-target nomination

    pinellolab/CRISPRme’s past year of commit activity
    Python 22 9 1 0 Updated Nov 10, 2025
  • simba-plus Public

    SIMBA+

    pinellolab/simba-plus’s past year of commit activity
    Python 0 0 0 0 Updated Nov 9, 2025
  • CRISPR-HAWK Public

    Variant- and Haplotype-aware CRISPR guide design toolkit

    pinellolab/CRISPR-HAWK’s past year of commit activity
    Python 0 1 0 0 Updated Nov 7, 2025
  • pinellolab/CRISPR_Pipeline’s past year of commit activity
    Python 13 MIT 5 6 0 Updated Nov 6, 2025
  • 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 2 AGPL-3.0 0 3 0 Updated Oct 31, 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 31, 2025
  • CRISPR-CLEAR-data Public

    Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.

    pinellolab/CRISPR-CLEAR-data’s past year of commit activity
    Jupyter Notebook 0 AGPL-3.0 0 0 0 Updated Oct 23, 2025
  • cell2net Public

    Mapping multi-scale and genotype-specific gene regualtion

    pinellolab/cell2net’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Oct 21, 2025