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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 173 48

  2. CRISPResso2 CRISPResso2 Public

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

    Python 277 95

  3. haystack_bio haystack_bio Public

    Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

    HTML 45 11

  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 22 7

  6. MotifRaptor MotifRaptor Public

    Explore the effect of genetic variants on transcription factor binding sites

    Python 8 2

Repositories

Showing 10 of 53 repositories
  • pyrovelocity Public

    𝒫robabilistic modeling of RNA velocity ⬱

    pinellolab/pyrovelocity’s past year of commit activity
    Python 42 AGPL-3.0 5 11 19 Updated Nov 4, 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 28 7 0 0 Updated Nov 4, 2024
  • crispr-bean Public

    Base Editing screens' Activity-Normalized variant effect size estimation

    pinellolab/crispr-bean’s past year of commit activity
    Python 8 AGPL-3.0 1 1 0 Updated Nov 1, 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 277 95 30 4 Updated Oct 31, 2024
  • DNA-Diffusion Public

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

    pinellolab/DNA-Diffusion’s past year of commit activity
    Python 366 52 2 10 Updated Oct 31, 2024
  • CRISPRme Public
    pinellolab/CRISPRme’s past year of commit activity
    Python 18 8 5 0 Updated Oct 29, 2024
  • simba_pbg Public

    A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph

    pinellolab/simba_pbg’s past year of commit activity
    Python 1 0 1 1 Updated Oct 22, 2024
  • 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 21, 2024
  • simba Public

    SIMBA: SIngle-cell eMBedding Along with features

    pinellolab/simba’s past year of commit activity
    Python 55 BSD-3-Clause 7 6 1 Updated Oct 16, 2024
  • 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 2 0 Updated Oct 11, 2024
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