Spatial alignment of single cell transcriptomic data.
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Updated
Aug 24, 2023 - Jupyter Notebook
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.
Pipeline for SpatialTranscriptomics and 10X Visium data
A Julia package for single cell and spatial data analysis
Image processing pipeline for spatial projects
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
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"
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
A Julia package for single cell and spatial data analysis
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
Course Assignment on Clustering of Spatial Transcriptomics Data
Repo linked to our recent publication in Science Advances
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.
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