There are no reviews yet. Be the first to send feedback to the community and the maintainers!
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 experimentsSTREAM
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell datascATAC-benchmarking
Benchmarking computational single cell ATAC-seq methodsdictys
Context specific and dynamic gene regulatory network reconstruction and analysissimba
SIMBA: SIngle-cell eMBedding Along with featureshaystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis PipelineAmpUMI
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 OccurrencespychromVAR
A python package for chromVARCRISPRitz
Tool package to perform in-silico CRISPR analysis and assessmentPrimeDesign
Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!singlecellvr
CRISPRme
MotifRaptor
Explore the effect of genetic variants on transcription factor binding sitesSTREAM2
STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics datacrispr-bean
Base Editing screens' Activity-Normalized variant effect size estimationCRISPRlungo
Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangementsperturbvelo
SVG_Benchmarking
Benchmarking methods for identification of spatially variable genesMEGATRON
MEGA TRajectories of clONesbean_manuscript
Scripts for plots used in manuscriptSTREAM_web
STREAM interactive website stream.pinellolab.orgsimba_pbg
A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraphsimba_comparison
Scripts used for performance comparison in SIMBA manuscript.simstpy
A framework for simulation of spatially-resolved omics data using pythonscreen-simulation
Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target editspbl-comparison-study
Comparison of probablisitc programming languages in Python: PyStan, PyMC3, Edward, and PyroSTREAM_atac
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq dataperturb-tools
Analysis Framework for Pooled CRISPR Genome Editing ScreensCRISPR_WGS_Detection
Love Open Source and this site? Check out how you can help us