Spatial alignment of single cell transcriptomic data.

Code for the spatialLIBD R/Bioconductor package and shiny app

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Spatial Transcriptomics Dashboard

A Julia package for single cell and spatial data analysis

Pipeline for SpatialTranscriptomics and 10X Visium data

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

Image processing pipeline for spatial projects

Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue"

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

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)

A Julia package for single cell and spatial data analysis

Course Assignment on Clustering of Spatial Transcriptomics 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.

R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.

Repo linked to our recent publication in Science Advances

Convert your STDeconvolve-generated and EnrichR-decoded topics into Seurat spatial clustering information via AUCell