Package installation | Loading necessary libraries | Example run | Working with Seurat | Session info

Loading necessary libraries | PBMC-3K UMAP | PBMC-3K t-SNE | Aya | Chia-Jung | Vladimir Shitov | Session info

Example workfow for analysing gene expression changes in macrophage activation | Starting application | Preparing the dataset for analysis | Exploring the dataset | Differential gene expression | Advanced usage | Gene identifiers conversion with AnnotationDB | Pathway analysis with Enrichr | Metabolic network analysis with Shiny GAM | GSEA enrichment plot | Link sharing | Loading dataset options | Serving Phantasus | Options for servePhantasus | Preloaded datasets | Support for RNA-seq datasets | Pathway database for FGSEA | Annotation database for AnnotationDB tool | Feedback | Acknowledgments | Citation

Overiew of GESECA method | Analysis of time course data | Analysis of single-cell RNA-seq | Analysis of spatial transcriptomic data | Analysis of 10X visium spatial data | Analysis of 10X xenium spatial transcriptomics data | Session info

Introduction | Installation | Loading precomputed RNA-seq counts | Inferring sample groups | Working with GCT files | Session info

Loading necessary libraries | Quick run | Performance considerations | Using Reactome pathways | Starting from files | Over-representation test | Session info

Installation | Example workfow | Saving modules | Example on full data and full network | Networks | KEGG | Rhea | Combined network | Rhea lipid subnetwork | Misc | Supplementary gene files | Non-enzymatic reactions | Using exact solver | Running with no metabolite data | Running with no gene data | Using metabolite-level network | Pathway annotation

Using the DelayedArray infrastructure | Interface to HSDS (HDF Object Store)