Pinned Repositories
CRISPR-SURF
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
DNA-Diffusion
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
MotifRaptor
Explore the effect of genetic variants on transcription factor binding sites
PrimeDesign
Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!
scATAC-benchmarking
Benchmarking computational single cell ATAC-seq methods
simba
SIMBA: SIngle-cell eMBedding Along with features
STREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Pinello Lab's Repositories
pinellolab/DNA-Diffusion
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
pinellolab/CRISPResso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
pinellolab/dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
pinellolab/simba
SIMBA: SIngle-cell eMBedding Along with features
pinellolab/pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
pinellolab/AmpUMI
Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
pinellolab/EPInformer
code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
pinellolab/GRAFIMO
GRAph-based Finding of Individual Motif Occurrences
pinellolab/CRISPRitz
Tool package to perform in-silico CRISPR analysis and assessment
pinellolab/CRISPRme
pinellolab/CRISPR-SURF
pinellolab/crispr-bean
Base Editing screens' Activity-Normalized variant effect size estimation
pinellolab/CRISPRlungo
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
pinellolab/SVG_Benchmarking
Benchmarking methods for identification of spatially variable genes
pinellolab/bean_manuscript
Scripts for plots used in manuscript
pinellolab/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.
pinellolab/screen-simulation
Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits
pinellolab/CRISPR-millipede-target
Calculate the enrichment scores of CRISPR alleles and variants from direct target amplicon-sequencing data using Bayesian linear regression model "millipede".
pinellolab/perturb-tools
Analysis Framework for Pooled CRISPR Genome Editing Screens
pinellolab/simba_pbg
A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph
pinellolab/STREAM2_tutorials
Tutorials for STREAM2 https://github.com/pinellolab/STREAM2
pinellolab/ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
pinellolab/ACCESS-ATAC-seq
Scripts for ACCESS-ATAC-seq data
pinellolab/CRISPR-CLEAR-data
Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.
pinellolab/CRISPR-millipede-helper
Helper utility function for running CRISPR-millipede pipelines
pinellolab/CRISPR-millipede-pipelines
Repository contains the pipeline scripts and resources for running tools in the CRISPR-millipede suite at scale.
pinellolab/CRISPR_comparison
Snakemake workflow for comparing E-G links to experimental data
pinellolab/CRISPR_Pipeline
pinellolab/scvelo
pinellolab/Xeno-share
Script for xenograft SHARE-seq data