spatial-omics

There are 2 repositories under spatial-omics topic.

gustaveroussy / sopa
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
generalization memory-management pipeline spatial-omics spatial-transcriptomics snakemake spatialdata multiplexed-imaging
Language:Python 100
prabhakarlab / Banksy
BANKSY: spatial clustering
clustering-algorithm single-cell-omics spatial-omics
Language:R 57
wanglab-broad / ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
in-situ-sequencing spatial-transcriptomics single-cell-analysis spatial-omics bioinformatics cell-segmentation transcriptomics
Language:Jupyter Notebook 39
scverse / napari-spatialdata
Interactive visualization of spatial omics data
napari napari-plugin spatial-analysis spatial-omics visualization
Language:Python 36
nichecompass
Lotfollahi-lab / nichecompass
End-to-end analysis of spatial multi-omics data
deep-learning graph-neural-networks spatial-omics variational-autoencoder
Language:Python 32
Mr-Milk / SpatialTis
Spatial analysis toolkit for single cell multiplexed tissue data
single-cell spaital-analysis tissue spatial-distribution heterogeneity network hotspot imaging-mass-cytometry multiplexed-ion-beam-imaging cell-cell-interaction spatial-analysis spatial-omics
Language:Python 29
ttgump / spaVAE
Dependency-aware deep generative models for multitasking analysis of spatial genomics data
deep-learning gaussian-processes pytorch spatial-omics spatial-transcriptomics variational-autoencoder
Language:Jupyter Notebook 25
ys-zong / conST
conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics
contrastive-learning deep-learning graph-neural-networks spatial-omics
Language:Python 21
JEFworks-Lab / SEraster
Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
rstats spatial-analysis spatial-data-analysis spatial-omics spatial-transcriptomics
Language:R 15
quentinblampey / spatialdata_xenium_explorer
Interoperability between SpatialData and the Xenium Explorer
10xgenomics spatial-analysis spatial-omics spatialdata visualization
Language:Python 14
JEFworks-Lab / CRAWDAD
Cell-type Relationship Analysis Workflow Done Across Distances
proteomics spatial-analysis spatial-omics transcriptomics
Language:R 12
fanglu0411 / sgs
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
anndata mudata sgs spatial-omics zarr visualization genome-browser multimodal scatac sceqtl scrna single-cell schic scmethylc
Language:Shell 10
LiuLab-Bioelectronics-Harvard / ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
bioinformatics transcriptomics cell-segmentation single-cell-analysis spatial-transcriptomics spatial-omics in-situ-sequencing
Language:Jupyter Notebook 7
yezhenqing / spatial-live
A Lightweight & Versatile Visualization Tool for Spatial-Omics Data
data-visualization spatial-omics bioinformatics-tool single-cell-omics
Language:TypeScript 7
escheR
boyiguo1 / escheR
R package to visualize colocalization for single cell & spatially-resolved genomics data
multidimensional rstats single-cell spatial-omics visualization
Language:R 6
ZJUFanLab / SpaTrio
cell-cell-communication gene-regulation single-cell-multi-omics spatial-omics spatial-transcriptomics
Language:Python 6
C0nc / TAICHI
A Python package for the Scalable and accurate identification condition-relevant niches from spatial -omics data.
computational-biology machine-learning spatial-omics spatial-transcriptomics
Language:Jupyter Notebook 2
annkamsk / mvae
Multimodal Variational Autoencoder dedicated to omics data integration
bioinformatics multimodal-deep-learning omics-data-integration pytorch spatial-omics
Language:Jupyter Notebook 1
larry080201 / RESTORE_norm
Perform RESTORE normalization on multiplexed imaging data.
multiplexed-imaging normalization tissue-microarray-analysis spatial-omics
Language:Python 0