Nanostring-Biostats / CosMx-Analysis-Scratch-Space
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.
☆48Updated last 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
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆61Updated 2 years ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆100Updated 7 months ago
- R package for pathway analysis in scRNA-seq data☆67Updated 5 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆72Updated 5 months ago
- R package for semi-supervised single-cell data integration☆79Updated 11 months ago
- R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data☆26Updated 7 months ago
- Cell type pipes for R☆51Updated last year
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆67Updated 2 years ago
- BANKSY: spatial clustering☆82Updated 6 months ago
- From geospatial to spatial -omics☆84Updated last week
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆26Updated this week
- ☆68Updated this week
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆49Updated 4 months ago
- ☆30Updated last month
- Single Cell Cluster Evaluation☆87Updated 3 years ago
- Methods to discover gene programs on single-cell data☆96Updated 2 months ago
- Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…☆39Updated 3 years ago
- Pan-Cancer Single Cell Classifier☆63Updated 8 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 7 months ago
- Code repository for the Tumor Immune Cell Atlas (TICA) project☆62Updated 2 years ago
- ☆59Updated 5 years ago
- Unified access to several second-generation deconvolution methods☆65Updated last week
- Framework for sensitive DE testing (using neighbourhoods)☆63Updated 6 months ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆101Updated last year
- Capybara: A computational tool to measure cell identity and fate transitions☆57Updated 2 years ago
- An R package for performing cell typing in SMI and other single cell data☆33Updated last month
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆52Updated 5 months ago
- Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using h…☆44Updated last month
- Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".☆89Updated 4 months ago
- Significance analysis for clustering single-cell RNA-sequencing data☆108Updated 4 months ago