drieslab / awesome-spatial-data-analysis
Awesome list of tools and methods to perform spatial transcriptomic data analysis.
☆39Updated 3 years ago
Alternatives and similar repositories for awesome-spatial-data-analysis:
Users that are interested in awesome-spatial-data-analysis are comparing it to the libraries listed below
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 8 months ago
- Single cell omics biology annotations☆48Updated 3 weeks ago
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆71Updated last week
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 9 months ago
- Quasilinear data representations for single-cell omics data analysis☆42Updated last year
- Python implementation of Milo for differential abundance testing on KNN graph☆62Updated last year
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆51Updated 2 years ago
- Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics☆33Updated last month
- Probabilistic Alignment of Spatial Transcriptomics Experiments v.2☆34Updated last year
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆68Updated 3 weeks ago
- ☆46Updated 2 years ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- ☆22Updated 2 years ago
- 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
- BANKSY: spatial clustering☆86Updated 6 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆59Updated last month
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆36Updated 5 months ago
- Spatial direct messaging detected by bivariate Moran☆25Updated last month
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆67Updated 2 years ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆105Updated last week
- MAGIC - imputation and de-noising single-cell RNA seq data sets☆26Updated 5 years ago
- ☆114Updated 2 years ago
- ☆43Updated 3 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆61Updated 2 years ago
- Bayesian Analytics for Spatial Segmentation☆23Updated 4 months ago
- Metacells - Single-cell RNA Sequencing Analysis☆101Updated 4 months ago
- R implementation of GeneTrajectory☆51Updated 10 months ago
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆71Updated 2 months ago
- Direct estimation of mean and covariance from single cell RNA seq experiments☆96Updated last week
- Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…☆34Updated last year