Data from an R perspective | Variables | Samples | Annotations | Item Indexing | JSON Data (tips on matching R) | Examples | Data Preparation | Scatter 2D Chart | Stacked Bar Chart | Clustered Bar Chart | CanvasXpress clustering | Boxplot | Piping Support and Examples | Additional Information

Overview | Examples | Scatter 3D Plot | Scatter 2D Matrix Plot | Boxplot | Heatmap | Four-way Venn Diagram | Additional Information

Overview | Purpose | UI Sections | Features | New Application Template Generation | Built-in Conveniences | Responsive UI | Application Busy Indicator | Application Reset | Logging & Log Display | Alerting | Styling | Usage | Shiny Modules | downloadFile | downloadableTable | downloadablePlot | Creating a Sample Application | Step 1: Generate | Step 2: Run | Creating your Application | Step 1: Generate a Blank Application | Step 2: Run (optional) | Step 3: Customize | program/global.R | program/ui_sidebar.R | program/ui_sidebar_right.R | program/ui_body.R | program/server_local.R | program/server_global.R | Other | program/data (directory) | program/fxn (directory) | www/periscope_style.yaml | Additional Resources

Introduction and Setup | Demonstration Dataset: Rat Liver Slice Compound Treatments | Starting DGEobj creation | Limma/Voom Workflow Reference | Pre-processing | Low Intensity Filtering | Filter for Protein Coding Genes | DGE Analysis | edgeR Normalization | Define the Model Formula | Check for Surrogate Variables (unaccounted-for variation) | Run Voom and fit the model (lmFit) | Run Contrasts | Alternative FDR scores

Introduction | DGEobj Overview | DGEobj Nomenclature: Items, Types and Base Types | DGEobj Structure | Preserving the Original Data | Building a DGE data object | Demonstration Dataset: Rat Liver Slice Compound Treatments | Initializing a DGEobj from dataframes | Retrieve GEO data for GSE120804 | Prepare the Design Table | Retrieve Gene Annotation from Ensembl | Validate Dataframe Relationships | Instantiate the DGEobj | Some basic metadata about the project | additional descriptive attributes | Institutional attributes | Examining a DGE object | Inventory function | Examine DGEobj Metadata | DGEobj Length and Dimensions | Rownames and Colnames | Subsetting a DGEobj | Inventory of a DGEobj | Adding Items to a DGEobj | Alignment QC Example | A Workflow Example | Automating funArgs Entries | Batch addition of multiple items | Pre-defined Item Types | Adding a New Data Type | Accessing data in a DGEobj | Retrieve a single item | Retrieve multiple items | Ancillary Functions | Function baseType | Querying Metadata Stored in Attributes | Function rmItem | Function setAttributes | Function showMeta | Technical Information | Project Meta Data | Workflow attributes | Customizing the DGEobj Definition for New Data Types

Overview | Purpose | Features | Usage | Shiny Module Overview | downloadablePlotUI | downloadablePlot | Additional Resources

Overview | Purpose | Features | Usage | Shiny Module Overview | downloadableTableUI | downloadableTable | Sample Application | Additional Resources

Overview | Purpose | Features | Usage | Shiny Module Overview | downloadFileButton | downloadFile | Sample Application | Additional Resources