py-sigxtalk 0.1.2

Python rewrite of SigXTalk: Dissecting crosstalk induced by cell-cell communication

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py-sigxtalk

Python rewrite of SigXTalk: Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data.

Installation

pip install py-sigxtalk

Quick Start

import pysigxtalk as psx

# Load databases
rtf_db, tftg_db = psx.load_databases(species="human")

# Prepare inputs
inputs = psx.prepare_input(exp_mat, target_genes, lr_pairs, rtf_db, tftg_db)

# Run HGNN
pathways = psx.run_hgnn(inputs, epochs=10, device="cpu")

# Calculate PRS
prs_results = psx.compute_prs(inputs.exp_clu, pathways, n_estimators=10)

# Visualize
psx.plot_counts_histogram(prs_results)
psx.plot_counts_bar(prs_results, topk=20)
psx.plot_fid_spe(prs_results, key_tg="CD68")

Benchmark

Python vs R Correlation (PBMC3k dataset):

• Pearson Correlation: 0.9912

Visualization Gallery

Crosstalk Analysis:

Histogram	Bar Chart	Fid/Spe

Alluvial	Ridgeline	Chord

Network & Heatmaps:

CCI Chord	CCI Circle	Signal Contribution

Rec-TG Heatmap	Circular Bar

Examples

example/
├── quickstart.ipynb              # Full analysis workflow
├── benchmark.ipynb               # Python vs R comparison
├── data/                         # Input data & results
├── figures/                      # Generated figures
└── scripts/                      # Utility scripts

Citation

Hou, J. et al. Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data. Nature Communications (2025).