CellChat Exploration

Preprocess local data into a CellChat object

Seurat and AnnData objects are accepted as an input

Possibility to subset and adjust most of CellChat pipeline parameters

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Metadata column from which to subset:

Identities to keep:
(Keep it empty and PROCEED to avoid subsetting)

Sample column from metadata:

Cluster/Annotation column from metadata:

Database to use:

Interaction group:

Ensembl dataset to convert gene names from Ensembl ID to Gene Symbol:

Dataset

Only change when input object contains Ensembl ID

"Automatic" works on Human, Mouse and Zebrafish when selecting the corresponding CellChat database

Parameters for identifyOverExpressedGenes:

thresh.pc

thresh.fc

thresh.p

Parameters for computeCommunProb:

population.size

raw.use

type

trim

Parameters for filterCommunication:

min.cells

Parameters for computeCommunProbPathway:

thresh

Parameters for aggregateNet:

thresh

Parameters for netAnalysis_computeCentrality:

thresh

Parameters for identifyCommunicationPatterns:

k_outgoing

k_incoming

Name for processed CellChat object:

Use processed CellChat object as:

First dataset

Second dataset

Download CellChat .rds

Database to edit:

Type of data to edit:

Edition mode for ligand-receptor database
Add Edit Delete

Row to edit:

Column to edit:

New value:

Remove Row or Column

Row Column

Row/Column to remove:

Create Row or Column

Row Column

Row/Column name to create:

Name for processed Database object:

Download Database .rds

First dataset (Reference for differential)

Select remote folder:

Load remote data:

Load local data:

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Second dataset

Select remote folder:

Load remote data:

Load local data:

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Author information

Authors:
Benjamin Dornat (benjamin.dornat@univ-lyon1.fr)
Fabien Le Grand (fabien.legrand@cnrs.fr)
Lab:
NeuroMyoGène institute - MeLiS Unit

Citation

Suoqin Jin et al., CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics, Nature Protocols 2024

R information

System information

System packages

Preprocess local data into a CellChat object

Ensembl dataset to convert gene names from Ensembl ID to Gene Symbol:

Parameters for identifyOverExpressedGenes:

Parameters for computeCommunProb:

Parameters for filterCommunication:

Parameters for computeCommunProbPathway:

Parameters for aggregateNet:

Parameters for netAnalysis_computeCentrality:

Parameters for identifyCommunicationPatterns:

Edition mode for ligand-receptor database
Add Edit Delete

First dataset (Reference for differential)

Second dataset

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

Preprocess local data into a CellChat object

Ensembl dataset to convert gene names from Ensembl ID to Gene Symbol:

Parameters for identifyOverExpressedGenes:

Parameters for computeCommunProb:

Parameters for filterCommunication:

Parameters for computeCommunProbPathway:

Parameters for aggregateNet:

Parameters for netAnalysis_computeCentrality:

Parameters for identifyCommunicationPatterns:

Edition mode for ligand-receptor database Add Edit Delete

First dataset (Reference for differential)

Second dataset

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

SVG Physical Dimensions:

Edition mode for ligand-receptor database
Add Edit Delete