Welcome to DEBrowser’s documentation!

Contents:

• Quick-start Guide
  • Getting Started
  • Low Count Filtering
  • Batch Effect Correction and Normalization
  • DE Analysis
  • The Main Plots of DE Analysis
  • The Heatmap of DE Analysis
  • GO Term Plots
  • Data Tables
  • Quality Control Plots
  • Autoload Data via Hyperlink
• Installation Guide
  • Operating System Dependencies
• DE Analysis
  • Introduction
  • DESeq2
  • Un-normalized counts
  • Used parameters for DESeq2
  • EdgeR
  • Used parameters for EdgeR
  • Limma
  • Used parameters for Limma
  • ComBat
  • DEBrowser
  • References
• Heatmaps
  • Used clustering and linkage methods in heatmap
  • Used distance methods in heatmap
  • Interactive Heatmap
  • The Heatmap of DE Analysis
  • The Scale Option of Heatmap
• DEBrowser Modules
  • Demo Data
  • Example Modules
• DEBrowser Additions
• Examples
  • QC plots without Batch Effect Correction
  • QC plots after Batch Effect Correction
  • The Differential Expression Plots
  • GO Term Plots
  • Log2 fold change comparison for PPARα pathway
• Frequently asked questions (FAQ)
  • Why un-normalized counts?
  • Why am I getting error while uploading files?
  • Why some columns not showed up after upload?
  • Why am I getting error while uploading CSV/TSV files exported from Excel?
  • Why can’t I see all the background data in Main Plots?
  • Why am I getting error when I click on DE Genes in Go Term Analysis?
  • How to download selected data from Main plots/QC Plots/Heatmaps?

Indices and tables

• Index
• Module Index
• Search Page