gustaveroussy / sopa
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
☆141Updated this week
Related projects ⓘ
Alternatives and complementary repositories for sopa
- Spatial Single-Cell Analysis Toolkit☆74Updated this week
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆30Updated 6 months ago
- Join subcellular Visium HD bins into cells☆58Updated last week
- Integrated pipeline for multiplexed image analysis☆76Updated 2 weeks ago
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆50Updated 2 years ago
- Code used to benchmark Xenium☆40Updated 4 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆92Updated last week
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆69Updated 11 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆38Updated 2 weeks ago
- ☆98Updated 6 months ago
- Super-resolved spatial transcriptomics by deep data fusion☆67Updated last year
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆35Updated 4 months ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆115Updated 6 months ago
- Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab☆81Updated 3 weeks ago
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆70Updated 2 weeks ago
- ☆28Updated last month
- Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data proces…☆151Updated this week
- Spatial mapping of cell types by integration of transcriptomics data☆88Updated 2 years ago
- A pixel classification based multiplexed image segmentation pipeline☆86Updated 11 months ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆42Updated 2 years ago
- BANKSY: spatial clustering☆75Updated 3 months ago
- CZ CELLxGENE Discover Census☆86Updated this week
- ☆48Updated 3 years ago
- An open and interoperable data framework for spatial omics data☆236Updated this week
- ☆31Updated last month
- ☆33Updated 7 months ago
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆137Updated this week
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆44Updated this week
- Probabilistic Alignment of Spatial Transcriptomics Experiments☆78Updated last year
- Python package to perform enrichment analysis from omics data.☆166Updated 2 months ago