Spatial alignment of single cell transcriptomic data.
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Jul 1, 2025 - Jupyter Notebook
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visium
Here are 81 public repositories matching this topic...
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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Feb 11, 2026 - Python
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
workflow bioinformatics rna-seq pipeline nextflow image-processing spatial transcriptomics single-cell microscopy st 10x-genomics 10xgenomics nf-core spatial-transcriptomics visium
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Oct 28, 2026 - Nextflow
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
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Mar 26, 2026 - HTML
Code for the spatialLIBD R/Bioconductor package and shiny app
shiny rstats bioconductor golem 10xgenomics spatial-transcriptomics visium spatiallibd spatialexperiment
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Oct 16, 2026 - R
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.
machine-learning bioinformatics deep-learning gene-expression pytorch single-cell cancer-research digital-pathology pathology computational-pathology spatial-transcriptomics histopathology visium foundation-models xenium spatial-biology
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Oct 26, 2026 - Jupyter Notebook
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
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Aug 14, 2026 - HTML
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"
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Nov 30, 2023 - Jupyter Notebook
Pipeline for SpatialTranscriptomics and 10X Visium data
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Jul 22, 2025 - R
Image processing pipeline for spatial projects
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Aug 3, 2023 - MATLAB
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
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Aug 29, 2026 - Nextflow
Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy
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Oct 28, 2026 - R
A Julia package for single cell and spatial data analysis
bioinformatics data-viz scrna-seq starmap julia-package single-cell-omics spatial-transcriptomics scatac-seq merfish visium seqfish xenium cartana slideseq
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Aug 7, 2025 - Julia
A curated list of tools, foundation models, datasets and tutorials for spatial transcriptomics and single-cell analysis, ordered the way an analysis goes.
awesome bioinformatics deep-learning genomics computational-biology scrna-seq awesome-list single-cell single-cell-rna-seq spatial-transcriptomics merfish visium spatial-omics foundation-models xenium
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Oct 19, 2026
R package using ICA based method for spatial transcriptomics analysis (Visium/Slide-seq/CosMX/MERSCOPE)
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Oct 12, 2026 - R
Scalable spatial omics in the browser for hundreds of samples at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/
browser viewer spatial spatial-analysis spatial-data omics spatial-proteomics mcd histology spatial-transcriptomics zarr visium multiplexed-imaging imaging-mass-cytometry spatial-omics xenium spatial-biology
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Oct 30, 2026 - Python
AI agent skills for cancer biology and multi-omics research
bioinformatics tcga cancer-genomics rnaseq deseq2 single-cell cancer-research mutation-analysis scrnaseq claude multi-omics spatial-transcriptomics scanpy visium ai-agent claude-ai ai-skills claude-skills skill-md
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Sep 19, 2026 - Jupyter Notebook
A Julia package for single cell and spatial data analysis
data-viz julia-package single-cell-omics scrna-seq-analysis spatial-transcriptomics visium xenium cartana
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Jun 26, 2025 - Julia
A Flask web app for joint visualization of multimodal spatial transcriptomics data
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Oct 31, 2025 - JavaScript
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