User Help Pages
  • Welcome to the Help Pages for UCSC Xena
  • Tutorials
    • Basic Tutorial: Section 1
    • Basic Tutorial: Section 2
    • Basic Tutorial: Section 3
    • Advanced Tutorial: Section 1
    • Advanced Tutorial: Section 2
    • Tutorial: Tumor vs Normal
    • Tutorial: Viewing your own data
    • Live examples
  • How do I ...
    • How do I make a KM plot?
    • How do I compare tumor vs normal expression?
    • How do I remove null data (gray lines) from view?
    • How do I make subgroups?
    • How do I make more than 2 subgroups?
    • How do I make subgroups with geneA high and geneB high?
    • How do I compare gene expression between subgroups?
    • How do I compare gene expression between different cancer types?
    • How do I remove duplicate samples from a KM plot?
    • How do I view multiple types of cancer together?
    • How do I filter to just one cancer type
    • How do I view my data with the data from TCGA?
    • How do I change the color of a column?
    • How do I interact with the tooltip?
    • How do I cite UCSC Xena?
  • Overview of features
    • Visual Spreadsheet
      • Coloring for Mutation Columns
      • Coloring for Segmented Copy Number Columns
    • Kaplan Meier Plots
    • Chart & Statistics View
    • Filtering and subgrouping
      • Supported search terms for finding samples
    • Differential Gene Expression
    • GSEA
    • Genomic Signatures
    • Bookmarks
    • Download Data
    • Xena Single Cell
    • TumorMap
    • MuPIT
    • Accessing data through python
    • Transcript View
    • Xena Gene Set Viewer
  • Overview of public data
    • Types of data we have
    • TCGA
    • GDC
    • More studies
    • Choosing a study/cohort
  • FAQ
    • Xena Browser
    • Data and datasets
  • Viewing your own data
    • Getting Started
    • Probes/transcripts/identifiers we recognize
    • Data format specifications and supported biological data types
    • KM plots using data from a Local Xena Hub
    • Hubs for institutions, collaborations, labs, and larger projects
    • Loading data from the command line
    • FAQ/Troubleshooting Guide
  • Technical documentation
    • Setting up Xena for your institution
    • Deep Linking Into Xena
    • Metadata Specification
  • Contact us
  • Cite us
  • Data Use Agreement
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On this page
  • Basic Step-by-Step Tutorial
  • Advanced Step-by-Step Tutorial
  • Video Tutorials
  • Overview of Xena (2 min)
  • Beginner Tutorial (17 min)
  • Advanced Tutorial (55 min)
  • Workshop Cheatsheet/Handout
  • How do I ...
  • Request a workshop

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Tutorials

Step-by-step tutorials, videos, and other materials to get you started.

Last updated 5 months ago

Was this helpful?

Basic Step-by-Step Tutorial

Advanced Step-by-Step Tutorial

Video Tutorials

Overview of Xena (2 min)

Beginner Tutorial (17 min)

Advanced Tutorial (55 min)

Recording of tutorial given for NCI in May 2021. Includes closed captioning.

https://cbiit.webex.com/cbiit/lsr.php?RCID=acf4ea46dd9e41338662f0ba1ac59754

Workshop Cheatsheet/Handout

How do I ...

How do I ... guides are useful if you have a specific question.

Request a workshop

Workshops are a great way to teach a group of people how to use Xena. They can be 1-hour, 1/2-day, or 1-day in length. Currently we are only giving workshops remotely via Zoom or a similar technology. We give workshops both within the USA and internationally. Please contact us for more information: genome-cancer@soe.ucsc.edu

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Xena_Workshop_handout.pdf
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