WashU Epigenome Browser

Gateway to the epigenome. (Art by Ting Wang)

Contents:

• Use the Browser
  • The Top Menu
  • Genomic Region Locator
  • Operations in the Tracks View Container
  • Settings
  • Apps
  • Track management
  • Track Customization
  • Circlet view for chromatin interaction tracks
  • Offline mode
  • New version notice
• Tracks
  • Track groups based on file types and localtions of the track files
  • Configure your webserver to enable CORS
  • Prepare track files
  • Annotation Tracks
  • Variant Tracks
  • Numerical Tracks
  • Dynamic Sequence Tracks
  • Read Alignment BAM Tracks
  • Methylation Tracks
  • Categorical Tracks
  • Long range chromatin interaction
  • qBED Track
  • genome-align Track
  • Matplot Track
• Datahub
  • Example data hub
  • Example bigWig track
  • Example dynseq track
  • Example methylC track
  • Example categorical track
  • Example longrange track
  • Example bigInteract track
  • Example repeatmasker track
  • Example geneAnnotation track
  • Example bigbed track
  • Example bed track
  • Example refbed track
  • Example HiC track
  • Example cool track
  • Example genomealign track
  • Example qBED track
  • Example matplot track
  • Example g3d track
  • Example Ruler track
  • Track properties
• URL parameters
  • genome
  • hub
  • bundle
  • sessionFile
  • hicUrl
  • position
  • noDefaultTracks
  • datahub
  • session
• Local track files
  • View local files as tracks
  • View files or a folder as a datahub
• Text Tracks
  • bed
  • bedGraph
  • longrange
  • customized long-range format
  • What if the text file is huge?
• Dynamic Tracks
  • Use dynamic bedgraph format
  • Make dynamic plot track from user interface
  • Make dynamic plot track using data hub
  • Make dynamic HiC maps from the user interface
  • Make dynamic HiC maps using data hub
  • Make dynamic longrange chromatin interaction track
  • Make Dynamic bed track for annotation data
  • Make dynamic bed track using data hub
  • Dynamic track options
• View 3D Structure
  • 3D visualization video tutorial on YouTube
  • g3d format
  • g3d track
  • 3D viewer menu
  • Config 3D model data
  • Config 3D viewer layout
  • Highlighting & labeling
  • Interactivity on 3D model
  • Interactivity on tracks
  • Numerical painting
  • Annotation painting
  • Animations on 3D
  • Export 3D images
• Image Tracks
  • view human image data from IDR
  • view mouse image data from 4DN
• Statistical Tracks
  • boxplot
• Installation
  • Setup on MacOSX/Linux
  • Start the browser
  • Setup on Windows
  • Example commands for installation on a RHEL system
  • Setup your own backend API (optional)
  • Firebase setup
  • Use without firebase
• Use Docker
• Embedding
• Frontend code architeture
  • Quick tour
  • Suggested order of reading
  • Making a new track type
  • Performance tips
  • React (and other) gotchas
  • Lessons trying to refactor into WebWorkers
• Add a new genome
  • Prepare genome sequence file
  • Create the folder for genome configuration files
  • Add the new genome to the system
• The Comparative Epigenome Browser
  • Landing page
  • Select a reference genome and one or more secondary genomes
  • Organizing tracks on the WashU Epigenome Browser
  • Add data tracks to the Comparative Epigenome Browser
  • Example: create a human-mouse multiple tracks comparison view using the Comparative Epigenome Browser
• FAQ
  • Hard Reload
  • Data fetch failed
  • Use HTTP or HTTPS
  • Firebase fetal error
  • Can I use without setup Firebase?
  • Local track security
  • What’s the different between hub and sessionFile URL parameter
  • Publish with the browser
• Contact us
  • Source code and issue tracker
  • Get help on social media
  • Cite the browser

Indices and tables

• Index

• Search Page