Major Release CrossTalkeR 2.0

🔥 CrossTalkeR Realease v2.0 - New Features 🔥

• Statistical Filtering with Fisher’s Exact Test
  Filter cell-cell communication networks using Fisher’s test to identify statistically significant interactions.

• Volcano Plot Visualization
  Visualize results of the Fisher's test in a volcano plot

• Heatmap Visualization with Clustering
  Explore communication patterns across cell types using heatmaps, including clustering by interaction weights

• Comprehensive Topological Analysis
  Generate bar plots for the calculated network topological measures, separately for:

  • cell–cell interaction networks
  • cell-gene interaction networks

• Ligand–Receptor Enrichment Analysis with PROGENy
  Step-by-step tutorial for pathway enrichment analysis of ligand–receptor pairs using PROGENy.

• Modeling Intracellular Communication
  Extend the communication network by incorporating transcription factors to model intracellular signaling.

• Integration with LIANA+
  Seamlessly using ligand-receptor interaction results from LIANA+. We provide a detailed tutorial on how to perform the integration Run liana

• Compatibility with scSeqComm
  Use scSeqComm outputs as inputs to the CrossTalkeR framework for downstream comparative analysis.

• CrossTalkeR Python
  Our package is now available in Python — bring differential cell-cell communication analysis to your Python environment! You can find more information in our Read the Docs. Integration with the scverse ecosystem is underway.

Release of new features

New Features 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

v1.3.5: Merge pull request #47 from CostaLab/lttf-devel

Pre-releasing the integrated CrossTalkeR

v1.3.2

updating docs

1.3.1

New input + Liana input compatibility

Updates

Merge pull request #31 from CostaLab/devel

updates

updates and new features

Merge pull request #5 from CostaLab/devel

v1.2

Adding barplots functions

v1.01.0

single condition updates

Release

Releasing the initial CrossTalkeR

Ligand Receptor crosstalk visualization tool pre-release

v0.99.7

Update README.md