Pinello Lab

pinellolab

Organization data from Github https://github.com/pinellolab

Massachusetts General Hospital/Harvard Medical School

Boston

Pinello Lab's repositories

DNA-Diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

Language:PythonNOASSERTION418 11 139

CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

Language:PythonNOASSERTION322 14 309

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

Language:PythonAGPL-3.0122 5 67

simba

SIMBA: SIngle-cell eMBedding Along with features

Language:PythonBSD-3-Clause63 3 19

pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

Language:PythonAGPL-3.049 5 211

EPInformer

code to run EPInformer for gene expression prediction and gene-enhancer link prediction

Language:Jupyter Notebook43 1 1

AmpUMI

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

Language:PythonMIT41 7 6

CRISPRitz

Tool package to perform in-silico CRISPR analysis and assessment

Language:PythonNOASSERTION32 5 15

GRAFIMO

GRAph-based Finding of Individual Motif Occurrences

Language:PythonMIT31 3 3

CRISPRme

Variant-aware CRISPR off-target nomination

Language:PythonNOASSERTION22 5 50

CRISPR-SURF

Language:PythonAGPL-3.017 1 5

CRISPR_Pipeline

Language:PythonMIT11 5 7

crispr-bean

Base Editing screens' Activity-Normalized variant effect size estimation

Language:PythonAGPL-3.09 2 13

crisprapido

use WFA2 to scan for CRISPR guide targets

Language:RustNOASSERTION5 30

CRISPRuno

Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements

Language:PythonNOASSERTION5 30

SVG_Benchmarking

Benchmarking methods for identification of spatially variable genes

Language:Jupyter NotebookMIT5 1 5

PerTurbo

Robust and efficient analysis of single-cell perturbation studies

Language:PythonMIT400

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.

Language:PythonAGPL-3.02 1 3

screen-simulation

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

Language:Python2 1 1

ACCESS-ATAC-seq

Scripts for ACCESS-ATAC-seq data

Language:PythonMIT1 20

CRISPR-millipede-target

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

Language:Jupyter NotebookAGPL-3.01 3 2

nf-core-accessatacseq

Language:NextflowMIT1 20

simba_pbg

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

Language:PythonNOASSERTION1 2 1

connect_jupyter_lab

Language:Shell000

CRISPR-CLEAR-data

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

Language:Jupyter NotebookAGPL-3.0030

CRISPR-HAWK

Variant- and Haplotype-aware CRISPR guide design toolkit

Language:PythonNOASSERTION000

CRISPR-millipede-helper

Helper utility function for running CRISPR-millipede pipelines

Language:Python030

docker-terra-jupter-python-mageck

Language:Dockerfile030

gradio-dna-diffusion

Language:HTMLNOASSERTION000

onboarding

Scripts for setting up new members' computing environments

Language:PowerShellMIT000