About | Load proteomics data | Format data | Loading image coordinates rom GEOJson | Create SpatialExperiment Object | Load lipidomics data | Retrieve metaspace data | Add image data | Comparing Protein and Lipids | Merging images to single coordinate system | Correlation analysis | Looking for lipids associated with known proteins | Ascribing function to unknown lipids | Plot proteins | Summary | Session info

R and other dependencies | Metagenomic data formatting requirements | Geographic map formatting requirements | Mapping soil locations to map | get the "Pixel" x/y (NOT lat/long x/y) of metagenome samples | Exporting the rasterized map | Examplary plotting | Using spammR on metagenomic geographic data | Sample Metadata | CLEANING UP OF DATA | Create SpatialExperiment object | Metagenomic differential expression and enrichment | Spatial heatmap showing abundance of significant KO | Pathway enrichment | Session Information

Getting started | Collecting data to analyze | Data overview and examples | Omics Measurement Data | Sample metadata | Image files | Omics metadata | Loading data into spatial experiment object. | Spatial data with image | Expression and pathway analysis | Differential expression | Plot differentially expressed proteins | Pathway enrichment measurements | Pathway plotting | Distance based measurements | Plot protein gradient | Gradient-based enrichment | Plotting pathways from gradient | Network plotting | Summary | References | Session info

Installation | Load libraries needed | Introduction | Definitions | Important points for consideration | Data normalization | Background | Multiple hypothesis correction | Pathway databases | Identifiers | Example data | Examples | Comparison of one condition/group versus another condition/group. | Caveat | Description | Interpretation | Fisher's exact test | Caveats | Visualizing Fisher's exact results | The Kolmogorov–Smirnov test (KS) | Visualizing KS test results | KS alternative: the one-sample Z test | Enrichment in Correlation | Visualizing correlation enrichment results | Phosphoproteomics data analysis | Visualizing kinase substrate enrichment

Load libraries needed | Load our test proteomics dataset | Compare enrichment methods

Load libraries needed | Example data | Figure 2