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.
☆88Updated 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:
- From geospatial to spatial -omics☆99Updated 3 weeks ago
- ☆96Updated 3 months ago
- AnnData interoperability in R☆135Updated last week
- marker-based purification of cell types from single-cell RNA-seq datasets☆134Updated 5 months ago
- Single Cell Cluster Evaluation☆98Updated 4 years ago
- R package for semi-supervised single-cell data integration☆92Updated last week
- Pan-Cancer Single Cell Classifier☆81Updated last year
- Framework for sensitive DE testing (using neighbourhoods)☆75Updated last month
- R package for Pathway RespOnsive GENe activity inference☆111Updated 2 years ago
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆81Updated 3 years ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆86Updated 3 years ago
- Significance analysis for clustering single-cell RNA-sequencing data☆122Updated last year
- Latent Embedding Multivariate Regression☆97Updated last year
- BANKSY: spatial clustering☆130Updated 2 months ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆113Updated last month
- Multiome GRN inference.☆131Updated last year
- Multiview Intercellular SpaTial modeling framework☆71Updated 6 months ago
- Direct estimation of mean and covariance from single cell RNA seq experiments☆124Updated 7 months ago
- R package for pathway analysis in scRNA-seq data☆76Updated last year
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆82Updated 9 months ago
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆151Updated 4 months ago
- AUCell: score single cells with gene regulatory networks☆179Updated last year
- ☆126Updated 3 years ago
- Metacell - Single-cell mRNA Analysis☆117Updated 11 months ago
- R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …☆118Updated 3 weeks ago
- Analysis of cell-cell communication at single-cell resolution☆105Updated last year
- Unified access to several second-generation deconvolution methods☆88Updated last week
- Single-Cell Clustering Assessment Framework☆107Updated 2 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆67Updated last month
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆80Updated 11 months ago