All

68 repositories

CRISPRme
Public
Variant-aware CRISPR off-target nomination
Python
•
Other
•10•27•9•2•Updated Jul 22, 2026Jul 22, 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
•62•491•1•6•Updated Jul 21, 2026Jul 21, 2026
CRISPR_Pipeline
Public
Python
•
MIT License
•11•16•7•3•Updated Jul 21, 2026Jul 21, 2026
chorus
Public
Jupyter Notebook
•
MIT License
•8•44•1•0•Updated Jul 20, 2026Jul 20, 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
•16•129•0•2•Updated Jul 20, 2026Jul 20, 2026
EPInformer
Public
EPInformer workflows for gene-expression prediction from DNA sequence, epigenomic signals, and chromatin contacts.
Jupyter Notebook
•12•58•1•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
•0•5•3•0•Updated Jul 8, 2026Jul 8, 2026
CRISPRLungo
Public
Python
•
Other
•2•9•2•0•Updated Jun 30, 2026Jun 30, 2026
simba-plus
Public
SIMBA+
Python
•0•0•0•0•Updated Jun 25, 2026Jun 25, 2026
chorus-article
Public
Chorus blog post (2026-006) + agent reproduction harness: install Chorus, run the prompts, verify every claim.
HTML
•0•0•0•0•Updated Jun 23, 2026Jun 23, 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
•117•350•47•5•Updated Jun 12, 2026Jun 12, 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•8•0•0•Updated May 25, 2026May 25, 2026
cell2net
Public
Mapping multi-scale gene regualtion using single-cell multiome
Python
•
MIT License
•2•2•1•1•Updated Apr 29, 2026Apr 29, 2026
ACCESS-ATAC
Public
Python
•0•0•0•0•Updated Apr 15, 2026Apr 15, 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
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•40•5•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
•4•11•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
nf-core-accessatacseq
Public
Nextflow
•
MIT License
•1•1•0•0•Updated Jun 11, 2025Jun 11, 2025
crisprapido
Public
use WFA2 to scan for CRISPR guide targets
Rust
•
Other
•4•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

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Pinello Lab

All

All

68 repositories

CRISPRme

DNA-Diffusion

CRISPR_Pipeline

chorus

dictys

EPInformer

CRISPR-Correct

CRISPRLungo

simba-plus

chorus-article

CRISPResso2

CRISPR-HAWK

cell2net

ACCESS-ATAC

AmpUMI

PerTurbo

CRISPR-millipede-target

SVG_Benchmarking

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

All

All

Repositories list

68 repositories