# User Help Pages

## User Help Pages

- [Welcome to the Help Pages for UCSC Xena](https://ucsc-xena.gitbook.io/project/master.md): Tutorials, Live Examples, and How to pages for UCSC Xena
- [Tutorials and webinars](https://ucsc-xena.gitbook.io/project/tutorials.md): Step-by-step tutorials to get you started and our schedule of upcoming webinars
- [Webinars](https://ucsc-xena.gitbook.io/project/tutorials/webinars.md): Explore upcoming webinars and sign up to stay in the loop on new dates.
- [Basic Tutorial: Section 1](https://ucsc-xena.gitbook.io/project/tutorials/basic-tutorial-section-1.md): Learn to create your first views in Xena
- [Basic Tutorial: Section 2](https://ucsc-xena.gitbook.io/project/tutorials/basic-tutorial-section-2.md): Learn how to remove samples with no data, subgroup samples, and make Kaplan Meier plots
- [Basic Tutorial: Section 3](https://ucsc-xena.gitbook.io/project/tutorials/basic-tutorial-section-3.md): Learn how to use Chart View and add new columns of data to a view
- [Advanced Tutorial: Section 1](https://ucsc-xena.gitbook.io/project/tutorials/advanced-tutorial-section-1.md): Learn how to view whole chromosomes and view advanced datasets such as exon expression
- [Advanced Tutorial: Section 2](https://ucsc-xena.gitbook.io/project/tutorials/advanced-tutorial-section-2.md): Learn how to use the pick samples feature, how to view multiple genes in a single column, how to view a signature, and how to run a differential expression analysis
- [Tutorial: Tumor vs Normal](https://ucsc-xena.gitbook.io/project/tutorials/tutorial-tumor-vs-normal.md): Learn how to compare tumor samples to normal samples using our TCGA TARGET GTEx study
- [Tutorial: Viewing your own data](https://ucsc-xena.gitbook.io/project/tutorials/tutorial-viewing-your-own-data.md): Learn how to view your own data using data from the Chinese Glioma Genome Atlas (CGGA)
- [Live examples](https://ucsc-xena.gitbook.io/project/tutorials/live-examples.md): Live Examples of what types of visualizations and analyses you can perform using UCSC Xena
- [How do I ...](https://ucsc-xena.gitbook.io/project/how-do-i.md): Step-by-step instructions for our most common use cases
- [How do I make a KM plot?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-make-a-km-plot.md)
- [How do I compare tumor vs normal expression?](https://ucsc-xena.gitbook.io/project/how-do-i/tumor-vs-normal.md)
- [How do I remove null data (gray lines) from view?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-remove-null-data-gray-lines-from-view.md)
- [How do I make subgroups?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-make-subgroups.md)
- [How do I make more than 2 subgroups?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-make-more-than-2-subgroups.md)
- [How do I make subgroups with geneA high and geneB high?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-make-subgroups-with-4-groups.md)
- [How do I compare gene expression between subgroups?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-compare-gene-expression-between-subgroups.md)
- [How do I compare gene expression between different cancer types?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-compare-gene-expression-between-different-cancer-types.md)
- [How do I remove duplicate samples from a KM plot?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-remove-duplicate-samples-from-a-km-plot.md)
- [How do I view multiple types of cancer together?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-view-more-than-one-type-of-cancer-together.md): For users who wish to compare data across different types of cancer
- [How do I filter to just one cancer type](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-filter-to-just-one-cancer-type.md): For users who wish to use the datasets in a Pan-Can cohort but need to view just one cancer type.
- [How do I view my data with the data from TCGA?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-view-my-data-with-the-data-from-tcga.md): If you are adding in new samples, this will require you to combine outside of Xena and then load. If you are adding new data on samples we already have, then simply load the data into a Xena Hub.
- [How do I change the color of a column?](https://ucsc-xena.gitbook.io/project/how-do-i/how-do-i-change-the-column-color.md)
- [How do I interact with the tooltip?](https://ucsc-xena.gitbook.io/project/how-do-i/freeze-and-un-freeze-tooltip.md)
- [How do I cite UCSC Xena?](https://ucsc-xena.gitbook.io/project/how-do-i/cite-xena.md)
- [Overview of features](https://ucsc-xena.gitbook.io/project/overview-of-features.md): More details about all the features we have on Xena
- [Visual Spreadsheet](https://ucsc-xena.gitbook.io/project/overview-of-features/visual-spreadsheet.md): This dynamic, powerful, and flexible view is our default view into the data.
- [Coloring for Mutation Columns](https://ucsc-xena.gitbook.io/project/overview-of-features/visual-spreadsheet/mutation-columns.md): More information about how we color mutation columns
- [Coloring for Segmented Copy Number Columns](https://ucsc-xena.gitbook.io/project/overview-of-features/visual-spreadsheet/coloring-for-segmented-copy-number-columns.md)
- [Kaplan Meier Plots](https://ucsc-xena.gitbook.io/project/overview-of-features/kaplan-meier-plots.md)
- [Chart & Statistics View](https://ucsc-xena.gitbook.io/project/overview-of-features/chart-view.md)
- [Filtering and subgrouping](https://ucsc-xena.gitbook.io/project/overview-of-features/filter-and-subgrouping.md): How to find samples that you want to remove or keep in the view. How to make subgroups.
- [Supported search terms for finding samples](https://ucsc-xena.gitbook.io/project/overview-of-features/filter-and-subgrouping/supported-search-terms-for-finding-samples.md)
- [Differential Gene Expression](https://ucsc-xena.gitbook.io/project/overview-of-features/differential-gene-expression.md): Run a genome-wide differential gene expression analysis to compare groups of samples
- [GSEA](https://ucsc-xena.gitbook.io/project/overview-of-features/gsea.md): Run a genome-wide differential GSEA analysis to compare groups of samples
- [Genomic Signatures](https://ucsc-xena.gitbook.io/project/overview-of-features/genomic-signatures.md): Enter a genomic signature over a set of genes for a particular dataset
- [Bookmarks](https://ucsc-xena.gitbook.io/project/overview-of-features/bookmarks.md): Bookmarks are a great way to save a particular view in Xena, either for yourself or to share with others.
- [Download Data](https://ucsc-xena.gitbook.io/project/overview-of-features/download-data.md): There are 4 ways to download data
- [Xena Single Cell](https://ucsc-xena.gitbook.io/project/overview-of-features/xena-single-cell.md): Overview of how to view single cell data
- [TumorMap](https://ucsc-xena.gitbook.io/project/overview-of-features/tumormap.md): A tool developed by the Stuart Lab to view samples in a 2D layout
- [MuPIT](https://ucsc-xena.gitbook.io/project/overview-of-features/untitled.md): A 3D protein viewer developed by Rachel Karchin's lab
- [Accessing data through python](https://ucsc-xena.gitbook.io/project/overview-of-features/accessing-data-through-python.md)
- [Transcript View](https://ucsc-xena.gitbook.io/project/overview-of-features/transcript-view.md)
- [Xena Gene Set Viewer](https://ucsc-xena.gitbook.io/project/overview-of-features/gene-sets-about.md)
- [Overview of public data](https://ucsc-xena.gitbook.io/project/public-data-we-host.md)
- [Types of data we have](https://ucsc-xena.gitbook.io/project/public-data-we-host/types-of-data-we-have.md)
- [TCGA](https://ucsc-xena.gitbook.io/project/public-data-we-host/tcga.md)
- [GDC](https://ucsc-xena.gitbook.io/project/public-data-we-host/gdc.md): Information on Xena data from GDC release v41.0
- [More studies](https://ucsc-xena.gitbook.io/project/public-data-we-host/more-studies.md)
- [Choosing a study/cohort](https://ucsc-xena.gitbook.io/project/public-data-we-host/choosing-a-study-cohort.md)
- [FAQ](https://ucsc-xena.gitbook.io/project/faq.md)
- [Xena Browser](https://ucsc-xena.gitbook.io/project/faq/basic-xena-browser.md)
- [Data and datasets](https://ucsc-xena.gitbook.io/project/faq/advanced-data-and-datasets.md)
- [Viewing your own data](https://ucsc-xena.gitbook.io/project/local-xena-hub.md)
- [Getting Started](https://ucsc-xena.gitbook.io/project/local-xena-hub/getting-started.md): Step-by-step instructions to viewing your own data
- [Probes/transcripts/identifiers we recognize](https://ucsc-xena.gitbook.io/project/local-xena-hub/supported-gene-and-probe-names.md)
- [Data format specifications and supported biological data types](https://ucsc-xena.gitbook.io/project/local-xena-hub/data-format-specifications.md)
- [KM plots using data from a Local Xena Hub](https://ucsc-xena.gitbook.io/project/local-xena-hub/km-plots-using-data-from-a-local-xena-hub.md)
- [Hubs for institutions, collaborations, labs, and larger projects](https://ucsc-xena.gitbook.io/project/local-xena-hub/hubs-for-institutions-collaborations-labs-and-larger-projects.md)
- [Loading data from the command line](https://ucsc-xena.gitbook.io/project/local-xena-hub/loading-data-from-the-command-line.md)
- [FAQ/Troubleshooting Guide](https://ucsc-xena.gitbook.io/project/local-xena-hub/faq-troubleshooting-guide.md)
- [Technical documentation](https://ucsc-xena.gitbook.io/project/technical-documentation.md)
- [Setting up Xena for your institution](https://ucsc-xena.gitbook.io/project/technical-documentation/setting-up-xena-for-your-institution.md)
- [Deep Linking Into Xena](https://ucsc-xena.gitbook.io/project/technical-documentation/deep-linking-into-xena.md): How to programmatically specify Xena Browser views
- [Metadata Specification](https://ucsc-xena.gitbook.io/project/technical-documentation/metadata-specification-1.md): metadata (.json file) specification
- [Contact us](https://ucsc-xena.gitbook.io/project/contact-us.md): We'd love to hear from you!
- [Cite us](https://ucsc-xena.gitbook.io/project/cite-us.md): Please cite us! Citations are an important metric to our funders. Citing us helps us continue to support Xena.
- [Data Use Agreement](https://ucsc-xena.gitbook.io/project/data-use-agreement.md)