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New updates on version 2.1.2
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sqjin committed Feb 6, 2024
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# CellChat v2
## Version 2.1.0
- CellChat v2 now enables the [inferrence of cell-cell communication from multiple spatially resolved transcriptomics datasets](https://htmlpreview.github.io/?https://github.com/jinworks/CellChat/blob/master/tutorial/CellChat_analysis_of_multiple_spatial_transcriptomics_datasets.html). Users should update the previously calculated individual CellChat object for spatial transcriptomics data analysis via `updateCellChat` function.
- We add [Frequently Asked Questions (FAQ) when analyzing spatially resolved transcriptomics datasets](https://htmlpreview.github.io/?https://github.com/jinworks/CellChat/blob/master/tutorial/FAQ_on_applying_CellChat_to_spatial_transcriptomics_data.html), particularly on how to apply CellChat to different technologies of spatial transcriptomics data, including sequencing-based and in-situ imaging-based readouts. In addition, we redefine the `scale.factors` for easier interpretation when applying other spatial technologies. In version 2.1.1, we change `scale.factors` to `spatial.factors`, but users still can run the old CellChat object with `scale.factors`. Users can also update the old CellChat object.
- We add [Frequently Asked Questions (FAQ) when analyzing spatially resolved transcriptomics datasets](https://htmlpreview.github.io/?https://github.com/jinworks/CellChat/blob/master/tutorial/FAQ_on_applying_CellChat_to_spatial_transcriptomics_data.html), particularly on how to apply CellChat to different technologies of spatial transcriptomics data, including sequencing-based and in-situ imaging-based readouts. In addition, we redefine the `scale.factors` for easier interpretation when applying other spatial technologies. In version 2.1.1, we change `scale.factors` to `spatial.factors`, but users still can run the old CellChat object with `scale.factors`. Users can also update the old CellChat object.
- In version 2.1.2, we change `object@meta$slices` to `object@meta$samples` in order to allow the identification of consistent communication across samples using the updated function `filterCommunication`. Users need to update the old CellChat object using `updateCellChat`. The ECM-Receptor signaling is assumed as diffusible signaling by default when analyzing spatial transcriptomics.

CellChat v2 is an updated version that includes
- inference of spatially proximal cell-cell communication between interacting cell groups from spatially resolved transcriptomics
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