Welcome to CellphoneDB’s documentation.

For reporting bugs or other issues with CellphoneDB please use: https://github.com/ventolab/CellphoneDB/issues. For any other questions please contact us via contact@cellphonedb.org.

Tool Guide:

• Documentation
  • Novel features in v5
• Installation
• Analysis & Methods
  • METHOD 1. Retrieval of interaction expression means
  • METHOD 2. Statistical inference of interaction specificity
    • Cell subsampling for accelerating analyses (Optional METHOD 2)
  • METHOD 3. Retrieval of differentially expressed interactions
  • Inclusion of Spatial Information: Microenvironments
  • TF activity status: CellSign module
  • Interaction ranking: Scoring module
• Input files
  • Data format advice
  • Counts file
  • Meta file
  • DEGs file
  • Microenvironment file
• Output files
  • P-value (pvalues.txt), Mean (means.txt), Significant mean (significant_means.txt) and Relevant interactions (relevant_interactions.txt)
  • Deconvoluted (deconvoluted.txt)
• Interpreting the outputs
  • How to read and interpret the results?
  • Why values of clusterA-clusterB are different to the values of clusterB-clusterA?
  • How can I query my CellphoneDB results?
• DATABASE of interactions
  • Key features of CellphoneDB
  • Database design: input files
    • 1. “gene_input”
    • 2. “protein_input”
      • a. Location of the protein in the cell
      • b. Receptors and integrins
      • c. Membrane and secreted proteins not considered for the cell-cell communication analysis (“others”)
    • 3. “complex_input”
    • 4. “interaction_input”
    • 5. “transcription_factor_input”
  • User-defined database
• Plotting results
• Release notes
  • cellphonedb v4.1.0
  • cellphonedb-data v4.1.0
  • cellphonedb-data v4.0.0
  • cellphonedb v3.0.0
  • cellphonedb-data v3.0.0
• Tutorials
• FAQs
  • 1. What are the counts input files accepted?
  • 2. How to extract the CellphoneDB input files from a Seurat object?
  • 3. How to extract the CellphoneDB input files from a scanpy anndata?
  • 4. Should the input file with the count data be with HGNC symbols (gene names) or Ensembl IDs?
  • 5. What is the purpose of subsampling?
  • 6. What is the meaning of “Rank” in the “significant_means.txt” output file?
• Citing

API:

• Install Python and Jupyter Notebook
• Analyse Your Data using CellphoneDB methods
• Data Preparation Functions
  • Load User Files
  • Validate meta DataFrame
    • meta_preprocessor()
  • Validate counts DataFrame
    • counts_preprocessor()
  • Subsample the counts data
    • __init__()
    • subsample()
• Analysis Methods
  • Non-statistical Analysis Method
    • call()
  • Statistical Analysis Method
    • call()
  • Differentially Expressed Genes (DEGs) Analysis Method
    • call()
• Database Utility Functions
  • Display CellphoneDB Database Versions
    • get_remote_database_versions_html()
  • Generate Your Own Input Files
    • generate_all()
  • Create Local CellphoneDB Database File and Load it into Memory
    • get_interactions_genes_complex()
    • get_db_path()
    • create_db()
  • Search CellphoneDB interactions for genes/complexes
    • search()
    • get_html_table()

Indices and tables

• Module Index