Nanostring-Biostats / CosMx-Analysis-Scratch-SpaceLinks
This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
☆82Updated this week
Alternatives and similar repositories for CosMx-Analysis-Scratch-Space
Users that are interested in CosMx-Analysis-Scratch-Space are comparing it to the libraries listed below
Sorting:
- ☆95Updated last month
- From geospatial to spatial -omics☆98Updated last month
- AnnData interoperability in R☆122Updated this week
- R package for semi-supervised single-cell data integration☆90Updated 3 months ago
- BANKSY: spatial clustering☆125Updated last month
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆81Updated 7 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆83Updated 2 years ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆57Updated 2 weeks ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆131Updated 3 months ago
- Pan-Cancer Single Cell Classifier☆81Updated last year
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆67Updated last week
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆79Updated 9 months ago
- R package for pathway analysis in scRNA-seq data☆76Updated last year
- Multiview Intercellular SpaTial modeling framework☆71Updated 5 months ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆81Updated 3 years ago
- Latent Embedding Multivariate Regression☆97Updated 11 months ago
- Significance analysis for clustering single-cell RNA-sequencing data☆119Updated last year
- Single Cell Cluster Evaluation☆98Updated 4 years ago
- Analysis of cell-cell communication at single-cell resolution☆105Updated last year
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆33Updated last year
- Framework for sensitive DE testing (using neighbourhoods)☆74Updated this week
- Gene regulatory network containing signed transcription factor-target gene interactions☆90Updated 5 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆90Updated 4 months ago
- A Bayesian model for compositional single-cell data analysis☆180Updated 2 years ago
- Multiome GRN inference.☆130Updated last year
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆69Updated 5 months ago
- ☆31Updated 5 months ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆111Updated 2 weeks ago
- Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".☆128Updated last year
- Unified access to several second-generation deconvolution methods☆87Updated last week