User Help Pages
  • Welcome to the Help Pages for UCSC Xena
  • Tutorials and webinars
    • Webinars
    • 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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  • Introduction to Xena for bulk sequencing data: June 5th, 2025 10am-12pm PT
  • More webinars coming soon!

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  1. Tutorials and webinars

Webinars

Explore upcoming webinars and sign up to stay in the loop on new dates.

Introduction to Xena for bulk sequencing data: June 5th, 2025 10am-12pm PT

This webinar will be on June 5th, 2025, 10am-12pm PT.

In this webinar we will explore Xena's core functionalities for bulk sequencing data including

  • Visualizing mutation, expression, and copy number variation for a gene, group of genes, or chromosome

  • Visualizing clinical/phenotype data

  • Running a Kaplan-Meier survival analysis

  • Creating charts and analyses with accompanying statistics

  • Running a Differential Gene Expression analysis

All analyses will be done on publicly available data. As time permits, we’ll also do a brief demonstration of how to explore your own bulk sequencing data within Xena.

The webinar will run for 1.5 hours, followed by 30 minutes for Q&A.

Sign up here: https://ucsc.zoom.us/meeting/register/VnLfFkaPS26Uj22AyVyMfA

More webinars coming soon!

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Last updated 1 month ago

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