drieslab / awesome-spatial-data-analysisLinks
Awesome list of tools and methods to perform spatial transcriptomic data analysis.
☆46Updated 4 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
Sorting:
- Python implementation of Milo for differential abundance testing on KNN graph☆76Updated 9 months ago
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆88Updated 8 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆67Updated last month
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆66Updated 4 months ago
- Metacells - Single-cell RNA Sequencing Analysis☆116Updated last year
- Context specific and dynamic gene regulatory network reconstruction and analysis☆123Updated last week
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆81Updated 8 months ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆115Updated last year
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 3 years ago
- trajectory inference☆105Updated 10 months ago
- Single-Cell Clustering Assessment Framework☆107Updated 2 years ago
- Predict RNA velocity through deep learning☆71Updated last year
- TACCO: Transfer of Annotations to Cells and their COmbinations☆62Updated 3 months ago
- GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data☆66Updated 5 months ago
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆144Updated last week
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆80Updated 10 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆77Updated 2 months ago
- ☆126Updated 3 years ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 3 years ago
- R implementation of GeneTrajectory☆65Updated last year
- ☆46Updated last year
- ☆84Updated this week
- Probabilistic Alignment of Spatial Transcriptomics Experiments☆96Updated 9 months ago
- Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.☆79Updated 7 months ago
- ☆50Updated last month
- Gene group activity utility functions for Scanpy☆97Updated 11 months ago
- ☆131Updated 2 years ago
- Spatial mapping of cell types by integration of transcriptomics data☆98Updated 3 years ago
- Single cell omics biology annotations☆50Updated 7 months ago
- Multi-omic velocity inference☆113Updated last year