## Tutorials

### Tutorial Slides
These tutorial slides contain annoted screenshots to walk you through using the cBioPortal site.
1. Single Study Exploration [Google slides](https://docs.google.com/presentation/d/1_OGK69lO4Z62WaxHHkNYmWvY0LQN2v0slfaLyY1_IQ0) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%201%20Single%20Study%20Exploration.pdf)
2. Single Study Query [Google slides](https://docs.google.com/presentation/d/1y9UTIr5vHmsNVWqtGTVGgiuYX9wkK_a_RPNYiR8kYD8) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%202%20Single%20Study%20Query.pdf)
3. Patient View [Google slides](https://docs.google.com/presentation/d/1Jr_2yEfgjKBn4DBiXRk4kmhIbtsRp6gd0iD3k1fIUUk) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%203%20Patient%20View.pdf)
4. Virtual Studies [Google slides](https://docs.google.com/presentation/d/1rQE5rbFNdmup-rAtySHFxlLp3i4qa8SBA7MiQpMdn1I) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%204%20Virtual%20Studies.pdf)
5. Onco Query Language (OQL) [Google slides](https://docs.google.com/presentation/d/1U39xgVujtBodwW20qIfcGu4E5n2zzaKkl2KmzzHqj4A) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%205%20Onco%20Query%20Language.pdf)
6. Group Comparison [Google slides](https://docs.google.com/presentation/d/1P2boDph8IfpvjxoxDj_496CLHGtshzJnbbZhszPsmf4) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%206%20Group%20Comparison.pdf)
7. Pathways [Google slides](https://docs.google.com/presentation/d/1O5WGucz0lrfdY25b5QS6zaID_26i434EYXBluqZfT2g) | [PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Tutorial%207%20Pathways.pdf)

### Webinar Recordings
Recordings of live webinars from April & May 2020
1. Introduction to cBioPortal [youtube.com](https://www.youtube.com/watch?v=fPIAxH--cSo) | [bilibili.com](https://www.bilibili.com/video/BV1tf4y1m7Lp) | [Download PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Webinar%201%20Introduction%20to%20cBioPortal.pdf) | [View slides](https://drive.google.com/drive/folders/0B9KTQJAGhFhhRi1qaTdUWmpLQTA?resourcekey=0-9Mbxt9c_wEbaGRLnAaASlg&usp=sharing)
2. Mutation Details & Patient View [youtube.com](https://www.youtube.com/watch?v=uJsp9kd2jIk) | [bilibili.com](https://www.bilibili.com/video/BV1Qf4y1m7Lx) | [Download PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Webinar%202%20Mutation%20Details%20and%20Patient%20View.pdf) | [View slides](https://drive.google.com/drive/folders/0B9KTQJAGhFhhRi1qaTdUWmpLQTA?resourcekey=0-9Mbxt9c_wEbaGRLnAaASlg&usp=sharing)
3. Expression Data Analysis [youtube.com](https://www.youtube.com/watch?v=YUxVv6pkxD4) | [bilibili.com](https://www.bilibili.com/video/BV1HK4y1t7dE) | [Download PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Webinar%203%20Expression%20Data%20Analysis.pdf) | [View slides](https://drive.google.com/drive/folders/0B9KTQJAGhFhhRi1qaTdUWmpLQTA?resourcekey=0-9Mbxt9c_wEbaGRLnAaASlg&usp=sharing)
4. Group Comparison [youtube.com](https://www.youtube.com/watch?v=Tx4HZCrIe5c) | [bilibili.com](https://www.bilibili.com/video/BV1VZ4y1W76p) | [Download PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Webinar%204%20Group%20Comparison.pdf) | [View slides](https://drive.google.com/drive/folders/0B9KTQJAGhFhhRi1qaTdUWmpLQTA?resourcekey=0-9Mbxt9c_wEbaGRLnAaASlg&usp=sharing)
5. API & R Client [youtube.com](https://www.youtube.com/watch?v=Nq12o2i0yaw) | [bilibili.com](https://www.bilibili.com/video/BV1jz4y197iU) | [Download PDF](https://raw.githubusercontent.com/cBioPortal/cbioportal/master/docs/tutorials/cBioPortal%20Webinar%205%20API%20and%20R%20Client.pdf) | [View slides](https://drive.google.com/drive/folders/0B9KTQJAGhFhhRi1qaTdUWmpLQTA?resourcekey=0-9Mbxt9c_wEbaGRLnAaASlg&usp=sharing) | [Workshop code](https://github.com/cBioPortal/2020-cbioportal-r-workshop)

### How-To Videos
Short videos that show how to perform specific analyses or how to use specific pages.
1. Comparing samples based on expression level of a gene [youtube.com](https://www.youtube.com/watch?v=HTiKUXk0j0s)
2. Proteomic profiles in cBioPortal - An example based on cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) [youtube.com](https://www.youtube.com/watch?v=62qbjQOH9qc) 
3. Filtering and adding clinical data to Mutations tab [youtube.com](https://www.youtube.com/watch?v=q9No2073c5o)
4. Exploring the longitudinal evolution of individual patients [youtube.com](https://www.youtube.com/watch?v=Hbbs-tHh9LQ)
5. Using Onco Query Language (OQL) to query based on the expression level of genes [youtube.com](https://www.youtube.com/watch?v=kHlFXw2TMzc)
6. How to explore the data in a study [youtube.com](https://www.youtube.com/watch?v=N8ffDgkqDWc)
7. How to run a query for genes of interest [youtube.com](https://www.youtube.com/watch?v=MH-kY5usA70)
8. How to download data [youtube.com](https://www.youtube.com/watch?v=JId304dp3tc)
9. Navigating AACR GENIE - Biopharma Collaborative (BPC) dataset [youtube.com](https://www.youtube.com/playlist?list=PLE2tjlUyHL8Gn4ythnuvf2BxWJVpAxkMM)
10. Using Chromoscope to explore structural variants [youtube.com](https://www.youtube.com/watch?v=e378l2MmgKY)

### Documentation
* Frequently Asked Questions [FAQ](/user-guide/faq.md)
* Onco Query Language [OQL](/user-guide/oql.md)

### Publications
* de Bruijn et al. Cancer Research 2023 [PubMed](https://pubmed.ncbi.nlm.nih.gov/37668528/)
* Cerami et al. Cancer Discovery 2012 [PubMed](http://cancerdiscovery.aacrjournals.org/content/2/5/401.abstract)
* Gao et al. Science Signaling 2013 [PubMed](https://www.ncbi.nlm.nih.gov/pubmed/23550210)

### Tutorials by others
* cBioPortal Tutorial Series by Jackson Laboratory [youtube.com](https://www.youtube.com/watch?v=tWdrcZOiXc0&list=PLWNp6Z5dXDZ7yRyny8aypSwrArs6e0EJi)
* Using the Cancer Digital Slide Archive in cBioPortal by Nicole M. Rivera Acevedo [youtube.com (English)](https://www.youtube.com/watch?v=oP0GbWmfVWM) | [youtube.com (Spanish)](https://www.youtube.com/watch?v=QyOVCxjVIPU)
* Visualizing and Downloading RNASeq data from cBioPortal by Farhan Haq [youtube.com](https://www.youtube.com/watch?v=I3KiLCE35Mk&list=PLvK49Q0ARs91Ilonq_07n0q9Cd5pOsdJW)