spatial-transcriptomics

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)

an integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references

A bare bones tutorial on how to analyse spatial transcriptomics data from raw sequencing reads to visualising spatially distinct features

Computational biology/bioinformatics workflows, codes, tech & concept notes on NGS data

Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.

Investigate cell-cell signaling, by analyzing ligand-receptor interactions in spatial transcriptomic data

R toolkit for estimating the ligands-receptors interference of spatial transcriptomics

Repo linked to our recent publication in Science Advances

Personal research site of Jian Wu — Computational Lung Biology, single-cell/spatial genomics, lung aging & disease atlas research.

Spatial Omics Living review

This Github repository holds data, Notebooks and results of running SDePER on both Simulated and Real datasets, and Notebooks for figure panels in manuscript, as well as the codes for running other cell type deconvolution methods.

Code for IN-DEPTH

Python toolkit for H&E image analysis and spatial contour analysis.

Personal academic website of Ruoqing Feng

Multi-scale computational dissection of a pro-inflammatory complement-macrophage interaction circuit in rheumatoid arthritis tissue