Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
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 Jun 2024
![](https://github.com/jianhuupenn.png)
https://github.com/StatBiomed/SpatialDM
Spatial direct messaging detected by bivariate Moran
cell-cell-communication ligand-receptor-interaction spatial-correlation spatial-transcriptomics
Last synced: 17 Jun 2024
![](https://github.com/StatBiomed.png)
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: 17 Jun 2024
![](https://github.com/lhc17.png)
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: 17 Jun 2024
![](https://github.com/saezlab.png)
https://github.com/euxhenh/cellar
Interactive software tool for the assignment of cell types in single-cell studies.
clustering codex genomics genomics-visualization gui python sc-atac-seq sc-rna-seq singlecell spatial-transcriptomics
Last synced: 16 Jun 2024
![](https://github.com/euxhenh.png)
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: 16 Jun 2024
![](https://github.com/ZJUFanLab.png)
https://github.com/ZJUFanLab/bulk2space
a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
bulk-sequencing deep-learning scrna-seq spatial-transcriptomics
Last synced: 15 Jun 2024
![](https://github.com/ZJUFanLab.png)
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: 07 May 2024
![](https://github.com/Dana-Farber-AIOS.png)
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 2024
![](https://github.com/scverse.png)
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: 30 Apr 2024
![](https://github.com/saezlab.png)
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: 21 Mar 2024
![](https://github.com/saezlab.png)