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/.
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Updated
Sep 10, 2024 - R
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
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.
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
Example human brain data used for https://research.libd.org/visiumStitched/.
Course Assignment on Clustering of Spatial Transcriptomics Data
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
A Julia package for single cell and spatial data analysis
A Julia package for single cell and spatial data analysis
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"
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
Image processing pipeline for spatial projects
Pipeline for SpatialTranscriptomics and 10X Visium data
Code for the spatialLIBD R/Bioconductor package and shiny app
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
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.
Spatial alignment of single cell transcriptomic data.
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