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.
☆77Updated 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:
- ☆94Updated 2 weeks ago
- From geospatial to spatial -omics☆97Updated 2 weeks ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆124Updated 2 months ago
- Pan-Cancer Single Cell Classifier☆79Updated last year
- R package for semi-supervised single-cell data integration☆90Updated last month
- AnnData interoperability in R☆115Updated this week
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆144Updated 2 months ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆80Updated 3 years ago
- R package for Pathway RespOnsive GENe activity inference☆108Updated 2 years ago
- Framework for sensitive DE testing (using neighbourhoods)☆72Updated last year
- Multiview Intercellular SpaTial modeling framework☆68Updated 3 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆77Updated 8 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆81Updated 2 years ago
- AUCell: score single cells with gene regulatory networks☆169Updated last year
- Gene regulatory network containing signed transcription factor-target gene interactions☆87Updated 4 months ago
- R package for pathway analysis in scRNA-seq data☆75Updated last year
- BANKSY: spatial clustering☆121Updated last month
- Latent Embedding Multivariate Regression☆94Updated 10 months ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆110Updated 2 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆65Updated last month
- Single Cell Cluster Evaluation☆97Updated 4 years ago
- scGSVA: Perform GSVA for single cell RNA seq☆65Updated 10 months ago
- A Shiny web app for mapping datasets using Seurat v4☆132Updated 11 months ago
- Significance analysis for clustering single-cell RNA-sequencing data☆119Updated last year
- Analysis of cell-cell communication at single-cell resolution☆104Updated last year
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆79Updated 6 months ago
- Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR☆93Updated last week
- Convert between AnnData and SingleCellExperiment☆140Updated this week
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆85Updated last year
- Coarse-graining of large single-cell RNA-seq data into metacells☆89Updated 3 months ago