#Visium

jfnavarro

st_pipeline

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

ratschlab

DeepSpot

DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.

10XGenomics

janesick_nature_comms_2023_companion

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"

ismms-himc

visium-clustergrammer2

Spatial Transcriptomics Dashboard