Pinello Lab's repositories
DNA-Diffusion
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
CRISPResso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
EPInformer
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
crispr-bean
Base Editing screens' Activity-Normalized variant effect size estimation
CRISPRlungo
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
bean_manuscript
Scripts for plots used in manuscript
SVG_Benchmarking
Benchmarking methods for identification of spatially variable genes
screen-simulation
Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits
perturb-tools
Analysis Framework for Pooled CRISPR Genome Editing Screens
CRISPR-millipede-sgRNA
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.
STREAM2_tutorials
Tutorials for STREAM2 https://github.com/pinellolab/STREAM2
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
ACCESS-ATAC-seq
Scripts for ACCESS-ATAC-seq data
CRISPR-millipede-helper
Helper utility function for running CRISPR-millipede pipelines
CRISPR-millipede-pipelines
Repository contains the pipeline scripts and resources for running tools in the CRISPR-millipede suite at scale.
CRISPR_comparison
Snakemake workflow for comparing E-G links to experimental data
openproblems-v2
Formalizing and benchmarking open problems in single-cell genomics
seqspec-parse
Parse a seqspec file for use with UMI-tools
Xeno-share
Script for xenograft SHARE-seq data