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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 assessmentCRISPR-SURF
PrimeDesign
Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!singlecellvr
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
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