Projects in Awesome Lists tagged with spatial-transcriptomics

https://github.com/scverse/squidpy

Spatial Single Cell Analysis in Python

data-visualization image-analysis single-cell-genomics single-cell-rna-seq spatial-analysis spatial-transcriptomics squidpy

Last synced: 07 May 2025

https://github.com/dana-farber-aios/pathml

Tools for computational pathology

biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics

Last synced: 29 Jan 2025

https://github.com/Dana-Farber-AIOS/pathml

Tools for computational pathology

biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics

Last synced: 06 May 2025

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/saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

bioinformatics data-science enrichment enrichment-analysis numba python single-cell spatial-transcriptomics transcriptomics

Last synced: 15 May 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: 28 Nov 2024

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: 05 Apr 2025

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: 23 Mar 2025

https://github.com/pachterlab/voyager

From geospatial to spatial -omics

bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics

Last synced: 10 Apr 2025

https://github.com/ZJUFanLab/SpaTalk

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

cell-cell-communication cell-cell-interaction graph-network knowledge-graph ligand-receptor-interaction single-cell spatial-data-analysis spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 30 Apr 2025

https://github.com/lmweber/osta

"Principles of Spatial (Transcript)omics Analysis with Bioconductor" book

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

Last synced: 27 Mar 2025

https://github.com/saezlab/mistyr

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 14 Jan 2025

https://saezlab.github.io/misty

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 14 Dec 2024

https://saezlab.github.io/mistyR/

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 30 Apr 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/StatBiomed/SpatialDM

Spatial direct messaging detected by bivariate Moran

cell-cell-communication ligand-receptor-interaction spatial-correlation spatial-transcriptomics

Last synced: 30 Apr 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: 23 Nov 2024

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: 23 Mar 2025

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/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/saezlab/dot

DOT

biology cell-type-deconvolution frank-wolfe gene-enrichment multi-objective-optimization optimization spatial spatial-transcriptomics

Last synced: 14 Apr 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/mictott/spotsweeper

Spatially-aware quality control for spatial transcriptomics

bioconductor quality-control spatial-transcriptomics

Last synced: 28 Jan 2025

https://github.com/gurbaaz27/cs690a-clustering-spatial-transcriptomics-data

Course Assignment on Clustering of Spatial Transcriptomics Data

cancer-genomics clustering computational-biology computational-genomics deep-learning gene-expression k-means-clustering leiden-algorithm louvain-algorithm rna-seq spatial-transcriptomics transcriptomics variational-autoencoder variational-autoencoders variational-inference visium

Last synced: 11 Apr 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: 23 Mar 2025

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/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