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Projects in Awesome Lists tagged with spatial-transcriptomics

A curated list of projects in awesome lists tagged with spatial-transcriptomics .

https://github.com/jinworks/cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

cell-cell-communication cell-cell-interaction microenvironment single-cell-analysis spatial-transcriptomics

Last synced: 14 Jan 2026

https://github.com/mahmoodlab/hest

Integrating histology and spatial transcriptomics - NeurIPS 2024

computational-pathology histology spatial-transcriptomics

Last synced: 12 Apr 2025

https://github.com/jianhuupenn/SpaGCN

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

graph-convolutional-network spatial-domains spatial-transcriptomics spatially-variable-genes

Last synced: 21 Jul 2025

https://github.com/rajewsky-lab/openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

bioinformatics omics spatial-transcriptomics transcriptomics

Last synced: 02 Feb 2026

https://github.com/lmweber/osta

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book

analysis-workflows bioconductor spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 26 Jan 2026

https://github.com/lieberinstitute/spatiallibd

Code for the spatialLIBD R/Bioconductor package and shiny app

10xgenomics bioconductor golem rstats shiny spatial-transcriptomics spatialexperiment spatiallibd visium

Last synced: 06 Oct 2025

https://github.com/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.

pipeline scrna-seq spatial-transcriptomics visium

Last synced: 17 Jan 2026

https://github.com/lieberinstitute/humanpilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

10xgenomics analysis biorxiv brain dlpfc human rstats spatial-transcriptomics visium

Last synced: 24 Aug 2025

https://github.com/altschulerwu-lab/muse

MUSE is a deep learning approach characterizing tissue composition through combined analysis of morphologies and transcriptional states for spatially resolved transcriptomics data.

clustering data-integration deep-learning multi-modal-analysis single-cell-ananlysis spatial-transcriptomics tensorflow

Last synced: 14 Dec 2025

https://github.com/JianYang-Lab/gsMap

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

gwas spatial-transcriptomics

Last synced: 29 Mar 2025

https://github.com/zijianni/spotclean

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

rna-seq spatial-transcriptomics

Last synced: 29 Oct 2025

https://github.com/wwxkenmo/enigma

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)

bulk-rna-seq-deconvolution cell-type-deconvolution cell-type-gene-expression-analysis deconvolution matrix-completion single-cell spatial-transcriptomics

Last synced: 12 Oct 2025

https://github.com/flatironinstitute/st_gridnet

A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

image-registration neural-networks spatial-transcriptomics tissue-registration visium-st

Last synced: 15 Jul 2025

https://github.com/lieberinstitute/spatialdlpfc

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

bioconductor dlpfc rstats spatial-transcriptomics spatialdlpfc transcriptomics visium visium-spg

Last synced: 31 Jan 2026

https://github.com/lima1/sttkit

Pipeline for SpatialTranscriptomics and 10X Visium data

10xgenomics spatial-transcriptomics visium

Last synced: 21 Jan 2026

https://github.com/lhc17/HoloNet

HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes

bioinformatics cell-cell-communication python spatial-transcriptomics

Last synced: 30 Apr 2025

https://github.com/mictott/spotsweeper

Spatially-aware quality control for spatial transcriptomics

bioconductor quality-control spatial-transcriptomics

Last synced: 11 Oct 2025

https://github.com/lambdamoses/novosparc

Reconstruction of spatial context of gene expression with optimal transport

in-situ optimal-transport single-cell spatial-transcriptomics

Last synced: 05 Apr 2025

https://github.com/jefworks-lab/scatterbar

Scatterbar - data visualization for proportional data across many spatially resolved coordinates

data-visualization spatial-analysis spatial-data-analysis spatial-transcriptomics

Last synced: 22 Oct 2025

https://github.com/pedrofale/tumorevo

Simulate tumor evolution and generate bulk and single-cell data from it.

cancer simulation single-cell spatial-transcriptomics tumor-evolution

Last synced: 28 Apr 2025

https://github.com/diegommcc/spatialddls

Deconvolution of spatial transcriptomics data based on Deep Learning

deconvolution deep-learning neural-network spatial-transcriptomics

Last synced: 22 Oct 2025

https://github.com/lieberinstitute/visium_spg_ad

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.

alzheimers-disease bioconductor rstats spatial-transcriptomics transcriptomics visium visium-spg visium-spg-ad

Last synced: 06 Jan 2026

https://github.com/earmingol/sccellfie

scCellFie offers advanced analysis of metabolic functions from single-cell and spatial transcriptomics. Efficient and user-friendly, it runs on Python and integrates with Scanpy, enabling single-cell and spatial analysis of metabolic tasks.

metabolic-modeling metabolic-pathways metabolism single-cell single-cell-transcriptomics spatial-transcriptomics systems-biology

Last synced: 13 Apr 2025

https://github.com/cafferychen777/flashdeconv

Fast Linear Algebra for Scalable Hybrid Deconvolution of Spatial Transcriptomics

bioinformatics cell-type-deconvolution computational-biology deconvolution python scanpy single-cell spatial-transcriptomics visium

Last synced: 13 Jan 2026

https://github.com/estfernan/boost

A collection of novel and standard statistical techniques for detecting spatially variable (SV) genes in spatial transcriptomics (ST) data.

bayesian-methods r r-package spatial-transcriptomics spatially-variable-genes

Last synced: 28 Jan 2026

https://github.com/thomasgust/elastic-st

A python data science library to build and analyze biological networks from spatial transcriptomics data. Allows inclusion of spatial information into the networks, going a step beyond graphs derived from scRNA-seq techniques.

bioinformatics biological-networks cython data-science linear-models machine-learning python spatial-transcriptomics spatial-transcriptomics-networks transcriptomics

Last synced: 26 Sep 2025

https://github.com/linjing-lab/stkan

Variational autoencoder with Kolmogorov-Arnold Network for spatial domain detection.

bioinformatics spatial-transcriptomics variational-autoencoder vision-transformer

Last synced: 14 Dec 2025

https://github.com/zhou-ran/scar

Spatially-resolved Chimeric AnalyzeR

cell-cell-interaction spatial-transcriptomics

Last synced: 19 Oct 2025

https://github.com/lieberinstitute/visiumstitched

R package containing functions useful for stitching Visium capture areas. Related to https://github.com/LieberInstitute/LS_visiumStitched

10xgenomics bioconductor rstats spatial-transcriptomics spatialexperiment spatiallibd visium

Last synced: 23 Mar 2025