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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 169 45

  2. CRISPResso2 CRISPResso2 Public

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

    Python 260 91

  3. haystack_bio haystack_bio Public

    Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

    HTML 44 10

  4. CRISPR-SURF CRISPR-SURF Public

    Python 15 3

  5. PrimeDesign PrimeDesign Public

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

    Python 21 6

  6. MotifRaptor MotifRaptor Public

    Explore the effect of genetic variants on transcription factor binding sites

    Python 8 2

Repositories

Showing 10 of 49 repositories
  • pyrovelocity Public

    𝒫robabilistic modeling of RNA velocity ⬱

    pinellolab/pyrovelocity’s past year of commit activity
    Python 38 AGPL-3.0 5 2 14 Updated Jul 30, 2024
  • CRISPRme Public
    pinellolab/CRISPRme’s past year of commit activity
    Python 16 8 3 0 Updated Jul 29, 2024
  • CRISPR-millipede-sgRNA 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-millipede-sgRNA’s past year of commit activity
    Python 0 0 2 0 Updated Jul 29, 2024
  • EPInformer Public

    code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

    pinellolab/EPInformer’s past year of commit activity
    Jupyter Notebook 7 0 0 0 Updated Jul 28, 2024
  • DNA-Diffusion Public

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

    pinellolab/DNA-Diffusion’s past year of commit activity
    Jupyter Notebook 351 49 5 10 Updated Jul 25, 2024
  • 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 260 91 27 5 Updated Jul 25, 2024
  • 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 Jul 17, 2024
  • dictys Public

    Context specific and dynamic gene regulatory network reconstruction and analysis

    pinellolab/dictys’s past year of commit activity
    Python 105 AGPL-3.0 14 1 0 Updated Jul 12, 2024
  • SVG_Benchmarking Public

    Benchmarking methods for identification of spatially variable genes

    pinellolab/SVG_Benchmarking’s past year of commit activity
    Jupyter Notebook 3 MIT 1 2 0 Updated Jul 5, 2024
  • ACCESS-ATAC-seq Public

    Scripts for ACCESS-ATAC-seq data

    pinellolab/ACCESS-ATAC-seq’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jul 3, 2024
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