Overview | Input Files | Gene Expression Data | Biological Network | Networks with no coordinates | Viewing Modes | Graphical User Interface (GUI) | Side panel | Results | Script Mode | Basic usage | Comparing multiple conditions (batch mode) | Signal transformation (signal_mode) | Two-color palettes | 3D Interactive Visualization | Importing from Differential Expression Tools | From DESeq2 | From edgeR | From limma | Checking the adapters without the tools | Quantitative Analysis of the Landscape | Node landscape scores | Automatic peak detection | Permutation significance test | Beyond the landscape test: replication and graph TFCE | Single-Cell RNA-seq (Seurat) | Toy datasets for testing and validation | Available datasets | Bimodal dataset | signal_mode = "logfc" with log2 microarray intensities | Multi-comparison (batch mode) and leviDiff | Real datasets from Bioconductor | RNA-seq: airway (DESeq2 + STRING) | Microarray: ALL (limma + STRING) | scRNA-seq: PBMC 10x (Seurat + STRING) | Building networks from STRING | Saving and reusing a downloaded network | Layout guide | Species codes | Full pipeline example (RNA-seq + STRING) | Session Information | Signal contracts and reproducibility | References

Introduction | Installation | Core concepts | The landscape score | The readExpColumn() helper | Signal transformation modes | Toy datasets | Hub topology | Gradient topology | Bimodal topology — simultaneous peak and valley | Flat expression — null control | Sparse expression — missing gene handling | Node scores and peak detection | Permutation significance test | Batch mode and multi-comparison | leviGrid — side-by-side comparison | leviDiff — landscape subtraction | Differential expression adapters | leviFromDESeq2 | leviFromEdgeR | leviFromLimma | leviFromSeurat | leviFromSE — SummarizedExperiment | Running the adapters here | Building networks from STRING | Layout algorithms | Species codes | Saving and reusing networks | Real-data examples | RNA-seq: airway (DESeq2 + STRING) | Microarray: ALL leukemia (limma + STRING) | scRNA-seq: PBMC (Seurat + STRING) | Enrichment analysis — leviEnrich | 3-D interactive visualization | Interactive GUI — LEVIui | Visualization parameters | Colour palettes | Session Information | Signal contracts and reproducibility | References

Why this vignette exists | Type I error under the global null | Power against effect size | How much does the layout matter? | A real dataset: dexamethasone in airway smooth muscle | The landscape and its node-label test | Replication: the sample-label tests | Is it the wiring? | Reproducing the study | Session information | References

Three nulls, three questions | Node-label null: the landscape test | The legacy cell mode | Sample-label null: biological replication | Paired designs and covariates | How small a design can be | Edge null: is it the wiring? | Autocorrelation on the graph | Running in parallel | Reporting checklist | Session information | References

Overview | Package Download and Installation | Graphical User Interface (GUI) | GFAG Path Viewer Function: GFAGpathUi() | GFAG Target Viewer Function: GFAGtargetUi() | Session Info | References

Overview | GFAGAnalysis | ADAnalysis | Session information | References