9 results found Sort:

gustaveroussy
sopa gustaveroussy
22
157
bsd-3-clause
6
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
pipeline snakemake spatialdata spatial-omics generalization memory-management multiplexed-imaging spatial-transcriptomics
Created 2023-09-04
1,076 commits to master branch, last one 21 hours ago
theMILOlab
SPATA2 theMILOlab
19
124
unknown
6
A Toolbox for Spatial Transcriptomics Analysis
data-analysis spatial-omics image-analysis spatial-transcriptomics
Created 2021-03-12
551 commits to master branch, last one about a month ago
fanglu0411
sgs fanglu0411
19
91
unknown
8
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
sgs zarr schic scrna mudata scatac sceqtl anndata scmethylc multimodal single-cell spatial-omics visualization genome-browser
Created 2024-07-01
68 commits to main branch, last one 15 days ago
prabhakarlab
Banksy prabhakarlab
12
82
other
4
BANKSY: spatial clustering
spatial-omics single-cell-omics clustering-algorithm
Created 2021-05-23
271 commits to bioc branch, last one 6 months ago
scverse
napari-spatialdata scverse
17
47
bsd-3-clause
13
Interactive visualization of spatial omics data
napari napari-plugin spatial-omics visualization spatial-analysis
Created 2022-04-02
332 commits to main branch, last one 10 days ago
EliHei2
segger_dev EliHei2
5
45
mit
2
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 imagin...
ai graphs xenium oncology segmentation spatial-omics molecule-graphs cell-segmentation single-cell-analysis graph-neural-networks spatial-transcriptomics
Created 2024-08-05
386 commits to main branch, last one 4 days ago
wanglab-broad
ClusterMap wanglab-broad
11
43
gpl-3.0
1
ClusterMap for multi-scale clustering analysis of spatial gene expression
spatial-omics bioinformatics transcriptomics cell-segmentation in-situ-sequencing single-cell-analysis spatial-transcriptomics
Created 2021-09-29
76 commits to main branch, last one 6 months ago
Lotfollahi-lab
nichecompass Lotfollahi-lab
6
39
bsd-3-clause
4
End-to-end analysis of spatial multi-omics data
deep-learning spatial-omics graph-neural-networks variational-autoencoder
Created 2022-07-15
886 commits to main branch, last one 19 days ago
ttgump
spaVAE ttgump
2
33
apache-2.0
1
Dependency-aware deep generative models for multitasking analysis of spatial genomics data
pytorch deep-learning spatial-omics gaussian-processes spatial-transcriptomics variational-autoencoder
Created 2022-11-25
92 commits to main branch, last one 6 months ago