All

67 repositories

chorus
Public
Python
•
MIT License
•1•5•0•14•Updated Apr 18, 2026Apr 18, 2026
simba-plus
Public
SIMBA+
Python
•1•0•0•0•Updated Apr 17, 2026Apr 17, 2026
CRISPR_Pipeline
Public
Python
•
MIT License
•6•13•8•0•Updated Apr 17, 2026Apr 17, 2026
CRISPResso2
Public
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
quantification genome-editing amplicon-sequences
quantification genome-editing amplicon-sequences
Python
•
Other
•114•336•53•3•Updated Apr 16, 2026Apr 16, 2026
DNA-Diffusion
Public
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
deep-learning genomics generative-model
deep-learning genomics generative-model diffusion-models regulatory-genomics stable-diffusion diffusion-probabilistic-models
Python
•
Other
•61•475•1•4•Updated Apr 16, 2026Apr 16, 2026
CRISPR-HAWK
Public
Variant- and Haplotype-aware CRISPR guide design toolkit
bioinformatics crispr genome-editing
bioinformatics crispr genome-editing crispr-design
Python
•
Other
•4•7•0•1•Updated Apr 16, 2026Apr 16, 2026
ACCESS-ATAC
Public
Python
•0•0•0•0•Updated Apr 15, 2026Apr 15, 2026
dictys
Public
Context specific and dynamic gene regulatory network reconstruction and analysis
network-inference network-visualization network-analysis
network-inference network-visualization network-analysis single-cell-analysis gene-regulatory-network dynamic-network single-cell-multiomics single-cell-network
Python
•
GNU Affero General Public License v3.0
•15•128•0•0•Updated Apr 14, 2026Apr 14, 2026
CRISPRme
Public
Variant-aware CRISPR off-target nomination
Python
•
Other
•10•24•1•1•Updated Apr 10, 2026Apr 10, 2026
CRISPRLungo
Public
Python
•
Other
•1•6•2•0•Updated Mar 25, 2026Mar 25, 2026
AmpUMI
Public
Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
Python
•
MIT License
•8•42•1•0•Updated Mar 20, 2026Mar 20, 2026
PerTurbo
Public
Robust and efficient analysis of single-cell perturbation studies
crispr-analysis crispr differential-expression
crispr-analysis crispr differential-expression functional-genomics single-cell-genomics single-cell-rna-seq regulatory-genomics
Python
•
MIT License
•2•15•1•2•Updated Mar 18, 2026Mar 18, 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
•0•2•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
EPInformer
Public
code to run EPInformer for gene expression prediction and gene-enhancer link prediction
Jupyter Notebook
•
MIT License
•12•52•0•1•Updated Jan 19, 2026Jan 19, 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
•0•4•3•0•Updated Jan 8, 2026Jan 8, 2026
cell2net
Public
Mapping multi-scale gene regualtion using single-cell multiome
Python
•
MIT License
•1•1•1•1•Updated Nov 28, 2025Nov 28, 2025
pyrovelocity
Public
Python
•
GNU Affero General Public License v3.0
•1•0•0•0•Updated Nov 20, 2025Nov 20, 2025
CRISPRitz
Public
Tool package to perform in-silico CRISPR analysis and assessment
Python
•
Other
•10•34•3•0•Updated Nov 17, 2025Nov 17, 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•0•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
screen bayesian-network crispr
screen bayesian-network crispr probabilistic-programming-language base-editing count-data-modeling ngs-sequencing-data
Python
•
GNU Affero General Public License v3.0
•3•10•1•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
nf-core-accessatacseq
Public
Nextflow
•
MIT License
•0•1•0•0•Updated Jun 11, 2025Jun 11, 2025
crisprapido
Public
use WFA2 to scan for CRISPR guide targets
Rust
•
Other
•3•6•0•6•Updated May 2, 2025May 2, 2025
docker-terra-jupter-python-mageck
Public
Dockerfile
•0•0•0•0•Updated Jan 10, 2025Jan 10, 2025
CRISPRuno
Public
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
Python
•
Other
•0•6•0•0•Updated Dec 21, 2024Dec 21, 2024

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Pinello Lab

All

All

67 repositories

chorus

simba-plus

CRISPR_Pipeline

CRISPResso2

DNA-Diffusion

CRISPR-HAWK

ACCESS-ATAC

dictys

CRISPRme

CRISPRLungo

AmpUMI

PerTurbo

CRISPR-millipede-target

SVG_Benchmarking

EPInformer

CRISPR-Correct

cell2net

pyrovelocity

CRISPRitz

CRISPR-CLEAR-data

CRISPR-millipede-helper

crispr-bean

connect_jupyter_lab

onboarding

ACCESS-ATAC-seq-deprecated

gradio-dna-diffusion

nf-core-accessatacseq

crisprapido

docker-terra-jupter-python-mageck

CRISPRuno

All

All

Repositories list

67 repositories