Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
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Updated
Jun 6, 2024 - Python
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
𝒫robabilistic modeling of RNA velocity ⬱
CellRank: dynamics from multi-view single-cell data
Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital
Predict RNA velocity through deep learning
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
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
collab | DFC
Tutorials for using BRIE
A guide to using a Seurat object in conjunction with RNA Velocity
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