Changelog

Source: NEWS.md

CrossTalkeR v1.4.0

• Splitted generate_report function in two parts:
  • analise_LR() to only run the analysis without generating the CrossTalkeR report
  • make_report() to only generate a new CrossTalkeR report for existing CrossTalkeR results
• Added node types to the network:
  • we now consider the annotation of a gene as ligand (L) or receptor (R) to consider the biological function
• Less constrains on the cell cluster name annotation (only ‘$’ must be avoided in the cluster naming)
• Integration with liana-py for ligand-receptor interaction predictions

CrossTalkeR v1.3.0

• Single and Comparative Reports
  • Cell Cell Interaction visualization
  • Sending and Receiving Cells Ranking
  • Gene Target based Sankey Plots
  • CCI and GCI PCA ranking
    • All measures and PC table
    • PC1 and PC2 based barplot
  • Leimkühler et. al. [2] data were added to the package
  • Fisher Test were implemented to highlight the CCI edges significance (new) 🔥NEW🔥
  • Change input format: Please see the Documentation 🔥NEW🔥
    • A python3 notebook are available to cast the old input to the new input.
  • Liana (Dimitrov et. al. [3]) Output can be used as CrossTalkeR input. 🔥NEW🔥
  • LR pair visualization plot can be done using a Seurat Object 🔥NEW🔥