rna-velocity

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

CellRank: dynamics from multi-view single-cell data

A guide to using a Seurat object in conjunction with RNA Velocity

Predict RNA velocity through deep learning

Toolkit for Single-Cell Velocity

𝒫robabilistic modeling of RNA velocity ⬱

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

Dynamical systems methods for RNA velocity analysis

Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments

Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.

Drop-in Rust + PyO3 acceleration of scvelo for single-cell RNA velocity

Module 4 for HKU Single-cell Workshop

Simulation based inference of differentiation trajectories from RNA velocity fields.

Entrain: Predicting Environmental Regulators of Differentiation Trajectories

Tutorials for using BRIE

R pacakge for RNA velocity estimation with nonlinear models

RNA velocity inference for single cell and spatial data

A Python package for mechanism-aware single-cell differential analysis. It partitions DE genes into transcription-driven versus stabilization-driven classes using nascent (unspliced) RNA residuals. Also supports conventional DE, functional enrichment (ORA, GSEA, GO, KEGG), and visualization.

Dockerized Velocyto for RNA Velocity

Single-cell RNA velocity and cell fate trajectory inference pipeline powered by scVelo, CellRank, and AnnData. Calculates directional mRNA splicing dynamics.