Cite our work | Quick start with demo data | New features | Overview | Installation | Get Started | Common uses for data visualization | Data integration | Integrated workflow with pathway analysis | Common Errors

Cite our work | Quick start with demo data | New features | Introduction | Installation | Get Started | Basic Analysis | Result Presentation and Intepretation | Advanced Analysis | Common Errors

Introduction | Cite our work | Quick start: RNA-Seq pathway analysis in about 40 lines | The native workflow | GO analysis and other gene set analyses | Per gene score choices | Joint workflows with common RNA-Seq analysis tools

Dataset: IFNg | Dataset cancer.ds (GSE16873) | ID mapping files | Molecule (or gene) IDs to glyphs IDs in SBGN-ML files: | Molecule (or gene) IDs to KEGG ortholog IDs | Molecule (or gene) IDs to pathway IDs

Introduction | Citation | Installation and quick start | Complete pathway analysis + visualization workflow | Load the gene (RNA-seq) data | Gene sets from SBGNview pathway collection | Load gene set for mouse with ENSEMBL gene IDs | Pathway or gene set analysis using GAGE | Visualize perturbations in top SBGN pathways | Calculate fold changes or gene perturbations | Visualize pathway perturbations by SBNGview | SBGNview with SummarizedExperiment object | Session Info

Overview | Citation | Installation | Prerequisites | Install SBGNview | Quick example | Additional information | Session Info

Overview | Citation | Installation and quick start | Getting started | Load the SBGNview package, together with pathview and other dependencies | Accessing help and documentation | SBGN pathway file (SBGN-ML) | Two tiers of support and two scenarios with SBGN based pathways | Load SBGNview's SBGN-ML pathway data collection | Information about the SBGN-ML pathway data collection | Search for pathways by keywords | Different layout for the same pathway | Custom SBGN-ML files | Basic visualization | Visualize gene data | Visualize compound data | Visualize both gene data and compound data | Work with SBGNview object | Structure of SBGNview object | Extract glyphs and arcs infromation from SBGNview object | Modify SBGNview object directly | Change output file name and format of SBGNview objects | Updating & modifying graphs | Hightlight nodes | Highlight all nodes | Highlight nodes by class | Show node IDs instead of node labels | Adjust node labels. | Label position, font size, color, change labels | Label text wrapping into multiple lines | When one input ID maps to multiple nodes | Highlight arcs and paths | Different layouts for the same pathway | SVG Editing Tool | ID mapping | Map between two types of IDs | Extract molecule list from pathways | Example using selected database | Use Reactome pathway database | Test SBGN reference cards | FAQs | Color key | Turn off color key | Session Info | References

Introduction | Expression data input | Gene set data input | Probe set ID conversion | gene or transcript ID conversion