Pinello Lab

All

66 repositories

cell2net
Public
Mapping multi-scale gene regualtion using single-cell multiome
Python
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MIT License
•0•0•1•0•Updated Nov 20, 2025Nov 20, 2025
pyrovelocity
Public
𝒫robabilistic modeling of RNA velocity ⬱
probabilistic-programming transcriptomics pyro probabilistic-models single-cell-genomics single-cell-rna-seq rna-velocity-estimation multiomics deep-generative-model developmental-trajectories
Python
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GNU Affero General Public License v3.0
•5•49•11•18•Updated Nov 20, 2025Nov 20, 2025
simba-plus
Public
SIMBA+
Python
•0•0•0•0•Updated Nov 19, 2025Nov 19, 2025
PerTurbo
Public
Robust and efficient analysis of single-cell perturbation studies
crispr-analysis crispr differential-expression functional-genomics single-cell-genomics single-cell-rna-seq regulatory-genomics
Python
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MIT License
•1•11•1•0•Updated Nov 19, 2025Nov 19, 2025
ACCESS-ATAC
Public
Python
•0•0•0•0•Updated Nov 19, 2025Nov 19, 2025
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
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GNU Affero General Public License v3.0
•0•1•1•1•Updated Nov 18, 2025Nov 18, 2025
CRISPRitz
Public
Tool package to perform in-silico CRISPR analysis and assessment
Python
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Other
•9•33•3•0•Updated Nov 17, 2025Nov 17, 2025
CRISPR_Pipeline
Public
Python
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MIT License
•5•13•6•0•Updated Nov 14, 2025Nov 14, 2025
CRISPR-HAWK
Public
Variant- and Haplotype-aware CRISPR guide design toolkit
bioinformatics crispr genome-editing crispr-design
Python
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Other
•1•0•0•0•Updated Nov 13, 2025Nov 13, 2025
CRISPRme
Public
Variant-aware CRISPR off-target nomination
Python
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Other
•9•22•1•0•Updated Nov 13, 2025Nov 13, 2025
CRISPResso2
Public
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
quantification genome-editing amplicon-sequences
Python
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Other
•108•323•45•3•Updated Nov 12, 2025Nov 12, 2025
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.
Python
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GNU Affero General Public License v3.0
•0•2•3•0•Updated Oct 31, 2025Oct 31, 2025
CRISPR-CLEAR-data
Public
Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.
Jupyter Notebook
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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
dictys
Public
Context specific and dynamic gene regulatory network reconstruction and analysis
network-inference network-visualization network-analysis single-cell-analysis gene-regulatory-network dynamic-network single-cell-multiomics single-cell-network
Python
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GNU Affero General Public License v3.0
•15•122•0•0•Updated Oct 8, 2025Oct 8, 2025
DNA-Diffusion
Public
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
deep-learning genomics generative-model diffusion-models regulatory-genomics stable-diffusion diffusion-probabilistic-models
Python
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Other
•54•422•2•5•Updated Oct 8, 2025Oct 8, 2025
CRISPRLungo
Public
Python
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Other
•0•2•0•0•Updated Oct 4, 2025Oct 4, 2025
EPInformer
Public
code to run EPInformer for gene expression prediction and gene-enhancer link prediction
Jupyter Notebook
•10•42•0•1•Updated Sep 23, 2025Sep 23, 2025
AmpUMI
Public
Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
Python
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MIT License
•9•41•1•0•Updated Aug 29, 2025Aug 29, 2025
crispr-bean
Public
Base Editing screens' Activity-Normalized variant effect size estimation
screen bayesian-network crispr probabilistic-programming-language base-editing count-data-modeling ngs-sequencing-data
Python
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GNU Affero General Public License v3.0
•2•9•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
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MIT License
•1•1•0•0•Updated Aug 1, 2025Aug 1, 2025
ACCESS-ATAC-seq-deprecated
Public
Scripts for ACCESS-ATAC-seq data
Python
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MIT License
•0•1•0•0•Updated Jul 8, 2025Jul 8, 2025
gradio-dna-diffusion
Public
HTML
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Other
•0•0•0•0•Updated Jul 1, 2025Jul 1, 2025
nf-core-accessatacseq
Public
Nextflow
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MIT License
•0•1•0•0•Updated Jun 11, 2025Jun 11, 2025
crisprapido
Public
use WFA2 to scan for CRISPR guide targets
Rust
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Other
•3•5•0•3•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
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Other
•0•5•0•0•Updated Dec 21, 2024Dec 21, 2024
simba_pbg
Public
A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph
Python
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Other
•0•2•1•1•Updated Oct 22, 2024Oct 22, 2024
simba
Public
SIMBA: SIngle-cell eMBedding Along with features
Python
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BSD 3-Clause "New" or "Revised" License
•7•63•7•1•Updated Oct 16, 2024Oct 16, 2024