dcjones / prosegLinks
Probabilistic cell segmentation for in situ spatial transcriptomics
☆134Updated this week
Alternatives and similar repositories for proseg
Users that are interested in proseg are comparing it to the libraries listed below
Sorting:
- Join subcellular Visium HD bins into cells☆126Updated this week
- ☆49Updated 4 months ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆81Updated this week
- BANKSY: spatial clustering☆124Updated last week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆139Updated 2 weeks ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆66Updated 3 weeks ago
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆65Updated 3 months ago
- ☆83Updated this week
- Metacells - Single-cell RNA Sequencing Analysis☆113Updated last year
- TACCO: Transfer of Annotations to Cells and their COmbinations☆61Updated last month
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆80Updated 7 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆168Updated 7 months ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆44Updated 3 weeks ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆133Updated 8 months ago
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 3 years ago
- AnnData interoperability in R☆119Updated this week
- Direct estimation of mean and covariance from single cell RNA seq experiments☆120Updated 5 months ago
- Spatial mapping of cell types by integration of transcriptomics data☆95Updated 3 years ago
- trajectory inference☆106Updated 9 months ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆89Updated last year
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆146Updated 2 months ago
- Convert between AnnData and SingleCellExperiment☆142Updated this week
- A Bayesian model for compositional single-cell data analysis☆177Updated 2 years ago
- Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab☆106Updated 3 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆74Updated 8 months ago
- Single-cell Lung Cancer Atlas with 1.2M cells☆69Updated 9 months ago
- Latent Embedding Multivariate Regression☆95Updated 11 months ago
- ☆22Updated this week
- Code used to benchmark Xenium☆69Updated last year
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆65Updated 4 months ago