dcjones / prosegLinks
Probabilistic cell segmentation for in situ spatial transcriptomics
☆90Updated this week
Alternatives and similar repositories for proseg
Users that are interested in proseg are comparing it to the libraries listed below
Sorting:
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆62Updated 2 weeks ago
- An R package for performing cell typing in SMI and other single cell data☆37Updated 2 weeks ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆67Updated last week
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆74Updated 2 years ago
- Identification of spatial homogeneous regions☆21Updated 4 months ago
- Join subcellular Visium HD bins into cells☆100Updated 2 weeks ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆37Updated 6 months ago
- ☆19Updated 2 weeks ago
- AnnData interoperability in R☆78Updated this week
- BANKSY: spatial clustering☆111Updated 2 months ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆74Updated 2 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 11 months ago
- Latent Embedding Multivariate Regression☆90Updated 6 months ago
- ☆28Updated 7 months ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆27Updated 10 months ago
- Single-cell spatial proteomics analysis that makes you happy!☆28Updated this week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆121Updated last week
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 2 years ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆35Updated last year
- Finding gene expression states in scRNA-seq data☆51Updated last year
- ☆44Updated last week
- ☆38Updated last month
- GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data☆53Updated 4 months ago
- ☆76Updated this week
- An R package for handling and analysing imaging mass cytometry data☆26Updated last week
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆42Updated 3 years ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆27Updated last week
- Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…☆19Updated last year
- From geospatial to spatial -omics☆93Updated 2 months ago
- ☆35Updated 2 weeks ago