Pinello Lab

All

53 repositories

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 9, 2024Nov 9, 2024
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
•1•8•1•0•Updated Nov 8, 2024Nov 8, 2024
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
•52•366•2•10•Updated Nov 8, 2024Nov 8, 2024
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•42•11•19•Updated Nov 7, 2024Nov 7, 2024
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
•95•277•30•4•Updated Nov 7, 2024Nov 7, 2024
EPInformer
Public
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
Jupyter Notebook
•7•30•0•0•Updated Nov 4, 2024Nov 4, 2024
CRISPRme
Public
Python
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Other
•8•18•5•0•Updated Oct 29, 2024Oct 29, 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•1•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•55•6•1•Updated Oct 16, 2024Oct 16, 2024
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•2•0•Updated Oct 11, 2024Oct 11, 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
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GNU Affero General Public License v3.0
•3•15•4•0•Updated Sep 4, 2024Sep 4, 2024
CRISPR-millipede-helper
Public
Helper utility function for running CRISPR-millipede pipelines
Python
•0•0•0•0•Updated Aug 29, 2024Aug 29, 2024
GRAFIMO
Public
GRAph-based Finding of Individual Motif Occurrences
bioinformatics motif-scanning haplotype-aware genome-variation-graphs genomic-variants
Python
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MIT License
•2•27•1•0•Updated Aug 29, 2024Aug 29, 2024
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
•14•111•1•0•Updated Aug 27, 2024Aug 27, 2024
ACCESS-ATAC-seq
Public
Scripts for ACCESS-ATAC-seq data
Python
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MIT License
•0•0•0•0•Updated Aug 23, 2024Aug 23, 2024
screen-simulation
Public
Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits
Python
•0•2•0•0•Updated Aug 15, 2024Aug 15, 2024
SVG_Benchmarking
Public
Benchmarking methods for identification of spatially variable genes
Jupyter Notebook
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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
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MIT License
•61•0•0•0•Updated Jul 8, 2024Jul 8, 2024
perturb-tools
Public
Analysis Framework for Pooled CRISPR Genome Editing Screens
Jupyter Notebook
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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
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MIT License
•0•0•0•0•Updated Jun 7, 2024Jun 7, 2024
scvelo
Public
Python
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BSD 3-Clause "New" or "Revised" License
•102•0•0•0•Updated Jun 1, 2024Jun 1, 2024
STREAM2_tutorials
Public
Tutorials for STREAM2 https://github.com/pinellolab/STREAM2
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated May 23, 2024May 23, 2024
AmpUMI
Public
Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
Python
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MIT License
•8•41•1•0•Updated May 7, 2024May 7, 2024
CRISPRitz
Public
Tool package to perform in-silico CRISPR analysis and assessment
Python
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Other
•9•22•3•0•Updated May 3, 2024May 3, 2024
bean_manuscript
Public
Scripts for plots used in manuscript
Jupyter Notebook
•1•3•0•0•Updated Apr 25, 2024Apr 25, 2024
CRISPRlungo
Public
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
Python
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Other
•0•5•0•0•Updated Apr 22, 2024Apr 22, 2024
STREAM2
Public
STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data
Python
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BSD 3-Clause "New" or "Revised" License
•0•9•3•1•Updated Apr 1, 2024Apr 1, 2024