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

STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

simba

SIMBA: SIngle-cell eMBedding Along with features

haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

AmpUMI

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

pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

GRAFIMO

GRAph-based Finding of Individual Motif Occurrences

pychromVAR

A python package for chromVAR

PrimeDesign

Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!

CRISPRitz

Tool package to perform in-silico CRISPR analysis and assessment

CRISPRme

CRISPR-SURF

singlecellvr

MotifRaptor

Explore the effect of genetic variants on transcription factor binding sites

STREAM2

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

CRISPRlungo

Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements

perturbvelo

MEGATRON

MEGA TRajectories of clONes

simba_comparison

Scripts used for performance comparison in SIMBA manuscript.

simba_pbg

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

simstpy

A framework for simulation of spatially-resolved omics data using python

CRISPR_WGS_Detection

perturb-tools

Analysis Framework for Pooled CRISPR Genome Editing Screens

STREAM2_tutorials

Tutorials for STREAM2 https://github.com/pinellolab/STREAM2

ismb_tutorial

plot_generation_CRISPRme

repo to generate CRISPRme plots for paper

rms_analysis

single cell data analysis for rms

simba_tutorials