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sqjin committed Nov 12, 2022
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## Update
Aug 06, 2022 (Version 1.5.0)
Nov 12, 2022 (Version 1.6.0)

We have now presented our comparison framework for systematically detecting dysregulated cell-cell communication across biological conditions, and
then utilized it to study the aging-induced signaling changes during skin wound healing. Our results not only present general communication rules and signaling mechanisms in wound healing associated with aging, but also provide a paradigm for other researchers to study cell-cell communication in other contexts. Please check out [our paper (Vu#, Jin#, Sun# et al., Cell Reports, 2022)](https://doi.org/10.1016/j.celrep.2022.111155) for the detailed methods and applications.
CellChat is now applicable to spatial imaging data. We showcase its application to 10X Visium data. When spatial locations of spots/cells are available, CellChat infers spatial-informed cell-cell communication between interacting cell groups. CellChat restricts cell-cell communication within the maximum interaction/diffusion length of molecules.

A brief [tutorial](https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/CellChat_analysis_of_spatial_imaging_data.html) for spatial imaging data analysis is available in the tutorial directory. CellChat's various functionality can be used for further data exploration, analysis, and visualization.

We have redesigned the structure of CellChat object. When loading previous CellChat object (version < 1.6.0), please update the object via `updateCellChat`.

For the version history and detailed important changes, please see the [NEWS file](https://github.com/sqjin/CellChat/blob/master/NEWS.md).

We will release the tutorial of applying CellChat to spatial transcriptomics data soon. Keep tuned!


## Capabilities
In addition to infer the intercellular communication from any given scRNA-seq data, CellChat provides functionality for further data exploration, analysis, and visualization.
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Please check the tutorial directory of the repo.

- [Full tutorial for CellChat analysis of a single dataset with detailed explanation of each function](https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/CellChat-vignette.html)
- [Brief tutorial for CellChat analysis of a single spatial imaging dataset](https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/CellChat_analysis_of_spatial_imaging_data.html)
- [Full tutorial for comparison analysis of multiple datasets](https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/Comparison_analysis_of_multiple_datasets.html)
- [Comparison analysis of multiple datasets with different cellular compositions](https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/Comparison_analysis_of_multiple_datasets_with_different_cellular_compositions.html)
- [Interface with other single-cell analysis toolkits (e.g., Seurat, SingleCellExperiment, Scanpy)](https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/Interface_with_other_single-cell_analysis_toolkits.html)
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