Pinello Lab

All

59 repositories

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
•
Other
•53•397•1•3•Updated Jun 29, 2025Jun 29, 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
•
GNU Affero General Public License v3.0
•5•47•10•17•Updated Jun 29, 2025Jun 29, 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
•
GNU Affero General Public License v3.0
•15•119•1•0•Updated Jun 27, 2025Jun 27, 2025
ACCESS-ATAC-seq
Public
Scripts for ACCESS-ATAC-seq data
Python
•
MIT License
•0•1•0•0•Updated Jun 25, 2025Jun 25, 2025
onboarding
Public
Scripts for setting up new members' computing environments
Shell
•
MIT License
•0•0•0•0•Updated Jun 24, 2025Jun 24, 2025
CRISPR_Pipeline
Public
Python
•
MIT License
•3•7•5•1•Updated Jun 20, 2025Jun 20, 2025
nf-core-accessatacseq
Public
Nextflow
•
MIT License
•0•1•0•0•Updated Jun 11, 2025Jun 11, 2025
CRISPResso2
Public
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
quantification genome-editing amplicon-sequences
Python
•
Other
•104•308•39•4•Updated Jun 10, 2025Jun 10, 2025
connect_jupyter_lab
Public
Shell
•0•0•0•0•Updated Jun 6, 2025Jun 6, 2025
CRISPRme
Public
Python
•
Other
•8•21•1•1•Updated May 8, 2025May 8, 2025
crisprapido
Public
use WFA2 to scan for CRISPR guide targets
Rust
•
Other
•2•1•0•2•Updated May 2, 2025May 2, 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
•
GNU Affero General Public License v3.0
•0•2•3•0•Updated Apr 30, 2025Apr 30, 2025
CRISPR-millipede-helper
Public
Helper utility function for running CRISPR-millipede pipelines
Python
•0•0•0•0•Updated Apr 26, 2025Apr 26, 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
•
GNU Affero General Public License v3.0
•2•9•1•2•Updated Feb 7, 2025Feb 7, 2025
docker-terra-jupter-python-mageck
Public
Dockerfile
•0•0•0•0•Updated Jan 10, 2025Jan 10, 2025
CRISPRlungo
Public
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
Python
•
Other
•0•5•0•0•Updated Dec 21, 2024Dec 21, 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".
Jupyter Notebook
•
GNU Affero General Public License v3.0
•0•1•1•1•Updated Nov 27, 2024Nov 27, 2024
EPInformer
Public
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
Jupyter Notebook
•10•43•0•1•Updated Nov 21, 2024Nov 21, 2024
simba_pbg
Public
A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph
Python
•
Other
•0•1•1•1•Updated Oct 22, 2024Oct 22, 2024
simba
Public
SIMBA: SIngle-cell eMBedding Along with features
Python
•
BSD 3-Clause "New" or "Revised" License
•7•63•7•1•Updated Oct 16, 2024Oct 16, 2024
CRISPR-CLEAR-data
Public
Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.
Jupyter Notebook
•0•0•0•0•Updated Sep 9, 2024Sep 9, 2024
CRISPR-SURF
Public
Python
•
GNU Affero General Public License v3.0
•3•17•4•0•Updated Sep 4, 2024Sep 4, 2024
GRAFIMO
Public
GRAph-based Finding of Individual Motif Occurrences
bioinformatics motif-scanning haplotype-aware genome-variation-graphs genomic-variants
Python
•
MIT License
•2•31•1•0•Updated Aug 29, 2024Aug 29, 2024
screen-simulation
Public
Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits
Python
•0•2•1•0•Updated Aug 15, 2024Aug 15, 2024
SVG_Benchmarking
Public
Benchmarking methods for identification of spatially variable genes
Jupyter Notebook
•
MIT License
•2•4•5•1•Updated Aug 12, 2024Aug 12, 2024
CRISPR_comparison
Public
Snakemake workflow for comparing E-G links to experimental data
R
•2•0•0•0•Updated Aug 6, 2024Aug 6, 2024
ABC-Enhancer-Gene-Prediction
Public
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
Python
•
MIT License
•68•0•0•0•Updated Jul 8, 2024Jul 8, 2024
perturb-tools
Public
Analysis Framework for Pooled CRISPR Genome Editing Screens
Jupyter Notebook
•
MIT License
•0•1•0•0•Updated Jul 2, 2024Jul 2, 2024
CRISPR-millipede-pipelines
Public
Repository contains the pipeline scripts and resources for running tools in the CRISPR-millipede suite at scale.
WDL
•0•0•0•0•Updated Jun 13, 2024Jun 13, 2024
Xeno-share
Public
Script for xenograft SHARE-seq data
Python
•
MIT License
•0•0•0•0•Updated Jun 7, 2024Jun 7, 2024