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

𝒫robabilistic modeling of RNA velocity ⬱

collab | DFC

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

Toolkit for Single-Cell Velocity

CellRank: dynamics from multi-view single-cell data

noSpliceVelo infers RNA velocity without separating unspliced and spliced transcripts

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

Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital

Predict RNA velocity through deep learning

Entrain: Predicting Environmental Regulators of Differentiation Trajectories

Simulation based inference of differentiation trajectories from RNA velocity fields.

Growth Hormone effect on Cartilage Growth Plate; Light-Sheet Microscopy; Pseudocoloring | Projects I started and still working on in Andrei Chagin Lab | Karolinska Institutet

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

IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

This repository contains coding scripts utilized for the analysis of Longitudinal scRNAseq of human pancreatic slices datasets

Tutorials for using BRIE

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

RNA Velocity for SEQC