Skip to content

@pinellolab Pinello Lab

All

    Repositories list

    71 repositories

    • CRISPRitz

      Public
      Tool package to perform in-silico CRISPR analysis and assessment
      C++
      •
      Other
      •11•43•0•2•Updated Nov 8, 2026Nov 8, 2026

    • crisprme-plus

      Public
      CRISPRme+ — web/data-manager + optimization successor lineage to CRISPRme
      crispr-analysiscrisprcrispr-target
      crispr-analysiscrisprcrispr-targetcrispr-cas9crispr-designcrispr-screens-pipeline
      Python
      •
      Other
      •1•3•0•3•Updated Nov 5, 2026Nov 5, 2026

    • DNA-Diffusion

      Public
      🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
      deep-learninggenomicsgenerative-model
      deep-learninggenomicsgenerative-modeldiffusion-modelsregulatory-genomicsstable-diffusiondiffusion-probabilistic-models
      Python
      •
      Other
      •63•491•1•6•Updated Oct 28, 2026Oct 28, 2026

    • CRISPR_Pipeline

      Public
      Python
      •
      MIT License
      •13•16•8•6•Updated Oct 28, 2026Oct 28, 2026

    • CRISPResso2

      Public
      Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
      quantificationgenome-editingamplicon-sequences
      quantificationgenome-editingamplicon-sequences
      Python
      •
      Other
      •120•359•49•2•Updated Oct 27, 2026Oct 27, 2026

    • PyroPPI

      Public
      Hierarchical Bayesian modelling of PPI Recorder screens
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 19, 2026Oct 19, 2026

    • chorus

      Public
      One interface to nine genomic deep-learning oracles — variant effect prediction, calibrated per-track percentiles, and plain-English analysis through MCP.
      bioinformaticsdeep-learninggenomics
      bioinformaticsdeep-learninggenomicsmcpvariant-effect-predictionregulatory-genomicsenformeralphagenome
      Python
      •
      MIT License
      •14•72•0•1•Updated Oct 15, 2026Oct 15, 2026

    • crisprme-skill

      Public
      Claude Code Agent Skill for running CRISPRme+ variant- and haplotype-aware CRISPR off-target searches from plain-language requests
      Python
      •0•0•0•0•Updated Oct 14, 2026Oct 14, 2026

    • CRISPRLungo

      Public
      Python
      •
      Other
      •4•13•0•0•Updated Oct 10, 2026Oct 10, 2026

    • CRISPRme

      Public
      Variant-aware CRISPR off-target nomination
      Python
      •
      Other
      •10•28•2•3•Updated Oct 8, 2026Oct 8, 2026

    • ACCESS-ATAC

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 29, 2026Sep 29, 2026

    • PerTurbo

      Public
      Robust and efficient analysis of single-cell perturbation studies
      crispr-analysiscrisprdifferential-expression
      crispr-analysiscrisprdifferential-expressionfunctional-genomicssingle-cell-genomicssingle-cell-rna-seqregulatory-genomics
      Python
      •
      MIT License
      •3•17•3•0•Updated Sep 24, 2026Sep 24, 2026

    • varaccess-igvf

      Public
      Python
      •1•2•0•0•Updated Aug 24, 2026Aug 24, 2026

    • cell2net

      Public
      Mapping multi-scale gene regualtion using single-cell multiome
      Python
      •
      MIT License
      •3•4•1•1•Updated Aug 6, 2026Aug 6, 2026

    • dictys

      Public
      Context specific and dynamic gene regulatory network reconstruction and analysis
      network-inferencenetwork-visualizationnetwork-analysis
      network-inferencenetwork-visualizationnetwork-analysissingle-cell-analysisgene-regulatory-networkdynamic-networksingle-cell-multiomicssingle-cell-network
      Python
      •
      GNU Affero General Public License v3.0
      •18•135•0•3•Updated Aug 3, 2026Aug 3, 2026

    • EPInformer

      Public
      EPInformer workflows for gene-expression prediction from DNA sequence, epigenomic signals, and chromatin contacts.
      Jupyter Notebook
      •13•64•0•0•Updated Jul 17, 2026Jul 17, 2026

    • 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-dist…
      Python
      •
      GNU Affero General Public License v3.0
      •1•5•3•0•Updated Jul 8, 2026Jul 8, 2026

    • chorus-article

      Public
      Chorus blog post (2026-006) + agent reproduction harness: install Chorus, run the prompts, verify every claim.
      HTML
      •1•1•0•0•Updated Jun 23, 2026Jun 23, 2026

    • CRISPR-HAWK

      Public
      Variant- and Haplotype-aware CRISPR guide design toolkit
      bioinformaticscrisprgenome-editing
      bioinformaticscrisprgenome-editingcrispr-design
      Python
      •
      Other
      •5•10•0•0•Updated May 25, 2026May 25, 2026

    • AmpUMI

      Public
      Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
      Python
      •
      MIT License
      •8•43•1•0•Updated Mar 20, 2026Mar 20, 2026

    • 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".
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •1•4•1•1•Updated Mar 8, 2026Mar 8, 2026

    • SVG_Benchmarking

      Public
      Benchmarking methods for identification of spatially variable genes
      Jupyter Notebook
      •
      MIT License
      •2•8•4•1•Updated Jan 27, 2026Jan 27, 2026

    • pyrovelocity

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •1•1•0•0•Updated Nov 20, 2025Nov 20, 2025

    • CRISPR-CLEAR-data

      Public
      Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Oct 23, 2025Oct 23, 2025

    • CRISPR-millipede-helper

      Public
      Helper utility function for running CRISPR-millipede pipelines
      Python
      •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • crispr-bean

      Public
      Base Editing screens' Activity-Normalized variant effect size estimation
      screenbayesian-networkcrispr
      screenbayesian-networkcrisprprobabilistic-programming-languagebase-editingcount-data-modelingngs-sequencing-data
      Python
      •
      GNU Affero General Public License v3.0
      •5•10•2•0•Updated Aug 13, 2025Aug 13, 2025

    • connect_jupyter_lab

      Public
      Shell
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • onboarding

      Public
      Scripts for setting up new members' computing environments
      PowerShell
      •
      MIT License
      •1•2•0•0•Updated Aug 1, 2025Aug 1, 2025

    • ACCESS-ATAC-seq-deprecated

      Public
      Scripts for ACCESS-ATAC-seq data
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 8, 2025Jul 8, 2025

    • gradio-dna-diffusion

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.