Pinello Lab

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

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

simba

SIMBA: SIngle-cell eMBedding Along with features

pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

AmpUMI

Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)

EPInformer

code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

GRAFIMO

GRAph-based Finding of Individual Motif Occurrences

CRISPRitz

Tool package to perform in-silico CRISPR analysis and assessment

CRISPRme

CRISPR-SURF

STREAM2

STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data

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

CRISPR-Correct

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.

screen-simulation

Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits

CRISPR-millipede-target

Calculate the enrichment scores of CRISPR alleles and variants from direct target amplicon-sequencing data using Bayesian linear regression model "millipede".

perturb-tools

Analysis Framework for Pooled CRISPR Genome Editing Screens

simba_pbg

A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph

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-CLEAR-data

Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.

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

scvelo

Xeno-share

Script for xenograft SHARE-seq data