Topic: "spatial-omics"
gustaveroussy/sopa
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
Language: Python - Size: 42 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 210 - Forks: 34
theMILOlab/SPATA2
A Toolbox for Spatial Transcriptomics Analysis
Language: R - Size: 1.04 GB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 142 - Forks: 20
prabhakarlab/Banksy
BANKSY: spatial clustering
Language: R - Size: 596 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 117 - Forks: 17
fanglu0411/sgs
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
Language: JavaScript - Size: 27.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 91 - Forks: 19
Lotfollahi-lab/nichecompass
End-to-end analysis of spatial multi-omics data
Language: Python - Size: 1.43 GB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 81 - Forks: 9
EliHei2/segger_dev
a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).
Language: Python - Size: 5.59 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 64 - Forks: 6
scverse/napari-spatialdata
Interactive visualization of spatial omics data
Language: Python - Size: 45.8 MB - Last synced at: 12 days ago - Pushed at: 13 days ago - Stars: 61 - Forks: 18
wanglab-broad/ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
Language: Jupyter Notebook - Size: 171 MB - Last synced at: 8 months ago - Pushed at: about 1 year ago - Stars: 41 - Forks: 11
JEFworks-Lab/CRAWDAD
Cell-type Relationship Analysis Workflow Done Across Distances
Language: R - Size: 970 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 31 - Forks: 4
Mr-Milk/SpatialTis 📦
Spatial analysis toolkit for single cell multiplexed tissue data
Language: Python - Size: 157 MB - Last synced at: about 18 hours ago - Pushed at: 11 months ago - Stars: 30 - Forks: 1
ZJUFanLab/scNiche
a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution
Language: Jupyter Notebook - Size: 12.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 26 - Forks: 2
ttgump/spaVAE
Dependency-aware deep generative models for multitasking analysis of spatial genomics data
Language: Jupyter Notebook - Size: 22.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 23 - Forks: 1
ys-zong/conST
conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics
Language: Python - Size: 5.94 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 18 - Forks: 4
JEFworks-Lab/SEraster
Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
Language: R - Size: 43.8 MB - Last synced at: 29 days ago - Pushed at: 3 months ago - Stars: 17 - Forks: 5
gao-lab/DECIPHER
DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data
Language: Python - Size: 12.4 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 15 - Forks: 0
quentinblampey/spatialdata_xenium_explorer
Interoperability between SpatialData and the Xenium Explorer
Language: Python - Size: 38.6 MB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 14 - Forks: 0
boyiguo1/escheR
R package to visualize colocalization for single cell & spatially-resolved genomics data
Language: R - Size: 101 MB - Last synced at: about 20 hours ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 2
yezhenqing/spatial-live
A Lightweight & Versatile Visualization Tool for Spatial-Omics Data
Language: TypeScript - Size: 233 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 0
LiuLab-Bioelectronics-Harvard/ClusterMap
ClusterMap for multi-scale clustering analysis of spatial gene expression
Language: Jupyter Notebook - Size: 300 MB - Last synced at: 8 months ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2
NFDI4BIOIMAGE/omero-vitessce
OMERO.web plugin for the Vitessce multimodal data viewer.
Language: Python - Size: 41.3 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 5 - Forks: 0
ZJUFanLab/SpaTrio
Language: Python - Size: 74.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1
C0nc/TAICHI
A Python package for the Scalable and accurate identification condition-relevant niches from spatial -omics data.
Language: Jupyter Notebook - Size: 9.43 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0
nf-core/sopa
Nextflow version of Sopa - spatial omics pipeline and analysis
Language: Nextflow - Size: 437 KB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 1
poncey/STForte
Enhanced spatially resolved transcriptomics analysis by matching between expression profiles and spatial topology.
Language: Jupyter Notebook - Size: 22.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1
donghongyu2020/SpaTranslator
SpaTranslator is a graph-based generative model for cross-modality prediction in spatial omics data. It enables the in silico generation of missing omics modalities—such as spatial ATAC-seq, RNA-seq, and histone modification profiles—across paired or unpaired tissue sections, by leveraging spatial neighborhood information and adversarial learning.
Language: Jupyter Notebook - Size: 1.56 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0
simonmfr/SPATA2 Fork of theMILOlab/SPATA2
A Toolbox for Spatial Transcriptomics Analysis
Language: R - Size: 1.04 GB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0
C0nc/River
A Python package for identification Differential Spatial Expression Pattern (DESP) gene by interpretable deep learning from multi-slice spatial omics data.
Language: Jupyter Notebook - Size: 19.5 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0
jeliason/SHADE
An R package for modeling asymmetric spatial associations between cell types in tissue images using a multilevel Bayesian framework.
Language: HTML - Size: 738 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0
zhaorui-bi/study_and_papers_for_spatial_omics_using_DL
Study and Paper Reading about Spatial Omics using Deep Learning
Size: 0 Bytes - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
Zhiliang-Bai/Patho-DBiT
Patho-DBiT is a platform to spatially decode RNA Biology in archival FFPE tissues.
Language: Python - Size: 568 KB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
annkamsk/mvae
Multimodal Variational Autoencoder dedicated to omics data integration
Language: Jupyter Notebook - Size: 544 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
