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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 176 50

  2. CRISPResso2 CRISPResso2 Public

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

    Python 298 102

  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 16 3

  5. PrimeDesign PrimeDesign Public

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

    Python 23 6

  6. MotifRaptor MotifRaptor Public

    Explore the effect of genetic variants on transcription factor binding sites

    Python 8 2

Repositories

Showing 10 of 57 repositories
  • pyrovelocity Public

    𝒫robabilistic modeling of RNA velocity ⬱

    pinellolab/pyrovelocity’s past year of commit activity
    Python 47 AGPL-3.0 5 10 17 Updated May 5, 2025
  • DNA-Diffusion Public

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

    pinellolab/DNA-Diffusion’s past year of commit activity
    Python 388 52 2 4 Updated May 5, 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 298 102 41 (1 issue needs help) 3 Updated May 2, 2025
  • crisprapido Public

    use WFA2 to scan for CRISPR guide targets

    pinellolab/crisprapido’s past year of commit activity
    Rust 1 2 0 2 Updated May 2, 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 Apr 30, 2025
  • pinellolab/CRISPR_Pipeline’s past year of commit activity
    Python 6 MIT 2 5 0 Updated Apr 29, 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 Apr 26, 2025
  • pinellolab/nf-core-accessatacseq’s past year of commit activity
    Nextflow 1 MIT 0 0 0 Updated Apr 1, 2025
  • CRISPRme Public
    pinellolab/CRISPRme’s past year of commit activity
    Python 21 8 2 1 Updated Mar 31, 2025
  • crispr-bean Public

    Base Editing screens' Activity-Normalized variant effect size estimation

    pinellolab/crispr-bean’s past year of commit activity
    Python 9 AGPL-3.0 2 1 2 Updated Feb 7, 2025