A spatial omics data analysis tool that enables both unsupervised and supervised discovery of complex tissue cellular neighborhoods from cell phenotypes.
☆25Jan 31, 2026Updated last month
Alternatives and similar repositories for CytoCommunity
Users that are interested in CytoCommunity are comparing it to the libraries listed below
Sorting:
- Deep fusion of spatial transcriptomics and histology images for interpretable high-definition embedding mapping☆17Feb 4, 2026Updated 3 weeks ago
- UNet script, model, sample data☆14Feb 19, 2025Updated last year
- Hotspot cluster distance analysis in spatial transcriptomic data☆35Feb 10, 2025Updated last year
- Biology-centered data-driven quality control for scRNA-seq☆19May 22, 2023Updated 2 years ago
- The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains☆34Apr 11, 2025Updated 10 months ago
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆33Apr 4, 2025Updated 10 months ago
- Gene Expression Decomposition and Integration☆19Feb 9, 2026Updated 3 weeks ago
- The `multiGSEA` R package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers.☆21Oct 30, 2025Updated 4 months ago
- Spatially constrained color profiling for visualizing single-cell resolution spatial data☆25Sep 23, 2024Updated last year
- ☆18Jun 3, 2020Updated 5 years ago
- stPlus: reference-based enhancement of spatial transcriptomics☆20Jan 6, 2024Updated 2 years ago
- SIMBA: SIngle-cell eMBedding Along with features☆20Jan 6, 2026Updated last month
- Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics☆49Apr 28, 2023Updated 2 years ago
- ☆25Feb 25, 2025Updated last year
- Quasilinear data representations for single-cell omics data analysis☆43May 4, 2023Updated 2 years ago
- CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data☆34Jul 24, 2025Updated 7 months ago
- Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:☆24Jun 8, 2021Updated 4 years ago
- Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)☆59Apr 3, 2024Updated last year
- QuPath extension to interactively align images☆26Aug 7, 2025Updated 6 months ago
- ☆31Jun 10, 2025Updated 8 months ago
- Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications☆64Mar 14, 2024Updated last year
- QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/☆28Dec 3, 2025Updated 2 months ago
- An Interpretable Self-Attention Network with block-attention and attention-attribution.☆12Sep 22, 2023Updated 2 years ago
- Single-cell epigenomic data annotation via supervised non-linear embedding☆24Apr 14, 2022Updated 3 years ago
- FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis☆23Oct 25, 2024Updated last year
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆71Nov 4, 2024Updated last year
- STHD: probabilistic cell typing of Single spots in whole Transcriptome spatial data with High Definition☆37Apr 30, 2025Updated 10 months ago
- ☆131Apr 24, 2024Updated last year
- An unsupervised scRNA-seq analysis workflow with graph attention networks☆25May 14, 2023Updated 2 years ago
- ☆33Jan 17, 2025Updated last year
- Official repository for Characterization of tumor heterogeneity through segmentation-free representation learning on multiplexed imaging …☆14Sep 28, 2025Updated 5 months ago
- Piecewise alignment for layers of mosaics☆36Feb 18, 2026Updated last week
- ☆32Aug 24, 2022Updated 3 years ago
- Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)☆30May 16, 2025Updated 9 months ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆39May 7, 2024Updated last year
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆138Feb 20, 2025Updated last year
- ☆11Updated this week
- A fast and accurate RNA secondary structure, end-to-end approach prediction method.☆12Jan 2, 2025Updated last year
- ☆10Sep 29, 2023Updated 2 years ago