dcjones / prosegLinks
Probabilistic cell segmentation for in situ spatial transcriptomics
☆142Updated last week
Alternatives and similar repositories for proseg
Users that are interested in proseg are comparing it to the libraries listed below
Sorting:
- ☆51Updated 5 months ago
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆86Updated this week
- Join subcellular Visium HD bins into cells☆129Updated last month
- AnnData interoperability in R☆130Updated this week
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆144Updated last week
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆67Updated last month
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆65Updated 5 months ago
- BANKSY: spatial clustering☆130Updated last month
- Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab☆108Updated 5 months ago
- Convert between AnnData and SingleCellExperiment☆142Updated this week
- Direct estimation of mean and covariance from single cell RNA seq experiments☆123Updated 7 months ago
- Bring your single-cell data to life☆88Updated 3 weeks ago
- GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data☆66Updated 5 months ago
- ☆24Updated 2 weeks ago
- ☆84Updated this week
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆47Updated 4 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆81Updated 8 months ago
- Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping☆91Updated last year
- Probabilistic Alignment of Spatial Transcriptomics Experiments v.2☆41Updated 9 months ago
- Latent Embedding Multivariate Regression☆97Updated last year
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆28Updated last year
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 3 years ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆81Updated 3 years ago
- Metacells - Single-cell RNA Sequencing Analysis☆116Updated last year
- From geospatial to spatial -omics☆99Updated this week
- Single-cell spatial proteomics analysis that makes you happy!☆48Updated this week
- Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…☆109Updated 2 weeks ago
- Python package for Probe set selection for targeted spatial transcriptomics.☆47Updated 3 weeks ago
- Identification of spatial homogeneous regions☆21Updated 2 months ago
- Spatial Single-Cell Analysis Toolkit☆104Updated 5 months ago