Projects in Awesome Lists by pinellolab
A curated list of projects in awesome lists by pinellolab .
https://github.com/pinellolab/dna-diffusion
🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
deep-learning diffusion-models diffusion-probabilistic-models generative-model genomics regulatory-genomics stable-diffusion
Last synced: 15 May 2025
https://github.com/pinellolab/crispresso2
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
amplicon-sequences genome-editing quantification
Last synced: 23 Apr 2026
https://github.com/pinellolab/scatac-benchmarking
Benchmarking computational single cell ATAC-seq methods
atac-seq bash benchmark jupyternotebook python r reproducible singlecell
Last synced: 03 Jul 2025
https://github.com/pinellolab/stream
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
lineage python scatac-seq scrna-seq singlecell trajectory visualization
Last synced: 03 Jul 2025
https://github.com/pinellolab/scATAC-benchmarking
Benchmarking computational single cell ATAC-seq methods
atac-seq bash benchmark jupyternotebook python r reproducible singlecell
Last synced: 11 May 2025
https://github.com/pinellolab/dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
dynamic-network gene-regulatory-network network-analysis network-inference network-visualization single-cell-analysis single-cell-multiomics single-cell-network
Last synced: 03 Aug 2025
https://github.com/pinellolab/pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming pyro rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-multiomics single-cell-rna-seq transcriptomics
Last synced: 06 Oct 2025
https://github.com/pinellolab/haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
cell chip-seq encode epigenetics epigenomics fimo gene gene-expression haystack-bio haystack-pipeline hotspot motif motifs plasticity regulation rna-seq roadmap specific-regions tfs transcription-factor-binding
Last synced: 06 Feb 2026
https://github.com/pinellolab/crispritz
Tool package to perform in-silico CRISPR analysis and assessment
Last synced: 06 Sep 2025
https://github.com/pinellolab/pychromvar
A python package for chromVAR
chromatin-accessibiity chromvar scatac-seq
Last synced: 03 Jul 2025
https://github.com/pinellolab/GRAFIMO
GRAph-based Finding of Individual Motif Occurrences
bioinformatics genome-variation-graphs genomic-variants haplotype-aware motif-scanning
Last synced: 10 May 2025
https://github.com/pinellolab/stream2
STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data
Last synced: 03 Jul 2025
https://github.com/pinellolab/motifraptor
Explore the effect of genetic variants on transcription factor binding sites
Last synced: 18 Oct 2025
https://github.com/pinellolab/crisprlungo
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements
Last synced: 09 Sep 2025
https://github.com/pinellolab/svg_benchmarking
Benchmarking methods for identification of spatially variable genes
Last synced: 23 Jun 2025
https://github.com/pinellolab/stream_web
STREAM interactive website stream.pinellolab.org
Last synced: 08 Sep 2025
https://github.com/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.
Last synced: 06 Mar 2026
https://github.com/pinellolab/simstpy
A framework for simulation of spatially-resolved omics data using python
atac-seq cite-seq cut-tag-seq multi-omics rna-seq simulation spatial
Last synced: 25 Feb 2026
https://github.com/pinellolab/perturb-tools
Analysis Framework for Pooled CRISPR Genome Editing Screens
Last synced: 03 Jul 2025
https://github.com/pinellolab/access-atac-seq
Scripts for ACCESS-ATAC-seq data
Last synced: 14 Aug 2025
https://github.com/pinellolab/crisprapido
use WFA2 to scan for CRISPR guide targets
Last synced: 03 Jul 2025
https://github.com/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".
Last synced: 09 Oct 2025
https://github.com/pinellolab/onboarding
Scripts for setting up new members' computing environments
Last synced: 23 Jun 2025
https://github.com/pinellolab/perturbo
Robust and efficient analysis of single-cell perturbation studies
crispr crispr-analysis differential-expression functional-genomics regulatory-genomics single-cell-genomics single-cell-rna-seq
Last synced: 10 Oct 2025
https://github.com/pinellolab/stream2_tutorials
Tutorials for STREAM2 https://github.com/pinellolab/STREAM2
Last synced: 21 Jul 2025
https://github.com/pinellolab/xeno-share
Script for xenograft SHARE-seq data
Last synced: 11 Sep 2025
https://github.com/pinellolab/crispr-millipede-pipelines
Repository contains the pipeline scripts and resources for running tools in the CRISPR-millipede suite at scale.
Last synced: 28 Jan 2026
https://github.com/pinellolab/crispr-clear-data
Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.
Last synced: 11 Aug 2025