# Research Analysis Platform

## Research Analysis Platform

- [About the Research Analysis Platform](https://dnanexus.gitbook.io/uk-biobank-rap/master.md)
- [About this documentation](https://dnanexus.gitbook.io/uk-biobank-rap/master/about-this-documentation.md)
- [Frequently asked questions](https://dnanexus.gitbook.io/uk-biobank-rap/master/frequently-asked-questions.md)
- [General FAQs](https://dnanexus.gitbook.io/uk-biobank-rap/master/frequently-asked-questions/general-faqs.md): Get answers to common questions about the Research Analysis Platform, and about UK Biobank data and systems.
- [500k WGS FAQs](https://dnanexus.gitbook.io/uk-biobank-rap/master/frequently-asked-questions/500k-wgs-faqs.md)
- [Quickstart](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/quickstart.md): Get started using the Research Analysis Platform.
- [Creating an account](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/quickstart/creating-an-account.md): Learn how to create a Research Analysis Platform account, access the Platform, and connect your account to the UK Biobank Access Management System.
- [Creating a project](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/quickstart/creating-a-project.md): Learn how to create a project and populate it with UK Biobank data.
- [Key concepts](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/key-concepts.md): Learn about the particularities of the Research Analysis Platform, and where to find detailed guidance on using its features.
- [Data structure](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/data-structure.md): Learn how UK Biobank data is organized and named on the Research Analysis Platform. Learn how to find and access bulk files and tabular data.
- [Data release versions](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/data-structure/data-release-versions.md): Get full details on data included in each UK Biobank Research Analysis Platform data release.
- [Updating dispensed data](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/data-structure/updating-dispensed-data.md)
- [Updating Projects for Participant Withdrawal](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/data-structure/updating-projects-for-participant-withdrawal.md)
- [Training videos](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/training-videos.md): Go in-depth with DNAnexus experts, who'll show you how to get the most out of the Research Analysis Platform.
- [General](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/training-videos/general.md): Learn about how to access UKB data and get started working on the UKB-RAP.
- [Tools](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/training-videos/tools.md): Learn about the different tools available on the UKB-RAP.
- [Analysis & data types](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/training-videos/analysis-and-data-types.md): Learn about using different data types and how to perform different analyses.
- [Roundtables](https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/training-videos/roundtables.md): Our roundtable webinars gather research experts to discuss different topics related to large-scale analysis and the UK Biobank dataset.
- [Accessing the Research Analysis Platform](https://dnanexus.gitbook.io/uk-biobank-rap/accessing-rap/accessing-the-research-analysis-platform.md)
- [2FA for UKB-RAP](https://dnanexus.gitbook.io/uk-biobank-rap/accessing-rap/2fa-for-ukb-rap.md)
- [Logging onto RAP](https://dnanexus.gitbook.io/uk-biobank-rap/accessing-rap/logging-onto-rap.md)
- [For Scientists](https://dnanexus.gitbook.io/uk-biobank-rap/cloud-computing/for-scientists.md)
- [For HPC Users](https://dnanexus.gitbook.io/uk-biobank-rap/cloud-computing/for-hpc-users.md)
- [Selecting an Instance Type](https://dnanexus.gitbook.io/uk-biobank-rap/cloud-computing/selecting-an-instance-type.md)
- [AWS Instance Types for UK Biobank](https://dnanexus.gitbook.io/uk-biobank-rap/cloud-computing/aws-instance-types-for-uk-biobank.md)
- [Using Project Spaces](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-platform/using-project-spaces.md)
- [Adding Users](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-platform/adding-users.md)
- [Copying Files Between Projects](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-platform/copying-files-between-projects.md)
- [Utilizing Metadata](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-platform/utilizing-metadata.md)
- [Downloading dx-toolkit](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-cli/downloading-dx-toolkit.md)
- [List of dx Commands](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-cli/list-of-dx-commands.md)
- [Logging onto RAP using dx-toolkit](https://dnanexus.gitbook.io/uk-biobank-rap/overview-of-the-cli/logging-onto-rap-using-dx-toolkit.md)
- [Costs and Billing](https://dnanexus.gitbook.io/uk-biobank-rap/administrator/billing-and-costs.md): Learn about how usage is billed on the Research Analysis Platform, how to set up a billing account to cover charges you’ll incur, your initial credit, and more.
- [Managing usage and storage costs](https://dnanexus.gitbook.io/uk-biobank-rap/administrator/managing-usage-and-storage-costs.md): Learn how to work cost-effectively on the Research Analysis Platform
- [Contact support](https://dnanexus.gitbook.io/uk-biobank-rap/administrator/technical-support.md): Contact the Research Analysis Platform Support team for help in using the Platform.
- [Service packages](https://dnanexus.gitbook.io/uk-biobank-rap/administrator/technical-support/service-packages.md): This FAQ addresses what's included with Standard Support on UKB-RAP, what's included with purchases of a UKB-RAP Service Package and how DNAnexus handles more complex queries.
- [Accessing data](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-data.md)
- [Accessing phenotype data](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-data/accessing-phenotypic-data.md): Learn how to export selected phenotypic fields into a TSV or CSV file, for easy browsing and analysis.
- [Using Spark to Analyze Tabular Data](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-data/using-spark-to-analyze-tabular-data.md): Learn to use Spark in JupyterLab to analyze UK Biobank tabular data.
- [Accessing bulk data](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/accessing-data/accessing-bulk-data.md): Learn how to search and analyze UK Biobank bulk data files.
- [Running analysis jobs](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs.md)
- [Tools library](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs/tools-library.md): The Research Analysis Platform provides a full-featured toolkit for preparing and analyzing a wide range of datatypes.
- [RStudio](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs/rstudio.md): Learn how to use RStudio Workbench, an interactive R development environment, on the DNAnexus Platform.
- [JupyterLab](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs/jupyterlab.md): These in-depth recorded webinars provide a detailed guide to leveraging the power of JupyterLab on the Research Analysis Platform.
- [SAIGE](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs/saige.md): A tool to perform genome-wide association tests in large-scale data sets and biobanks
- [Command-Line Interface](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs/command-line-interface.md): These short tutorial videos provide an in-depth guide to accessing and using the Research Analysis Platform via the command-line interface (CLI).
- [Custom app](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/running-analysis-jobs/custom-app.md): In many cases the Platform allows you to use apps and workflows you’ve developed in another environment. This page provides a rundown on how to import apps or workflows of a wide variety of types.
- [Managing jobs](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-jobs.md)
- [Job Priority](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-jobs/managing-job-priority.md): Learn how to determine what priority level is suited for your analysis, and how the different options affect job execution.
- [Troubleshooting guide](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-jobs/troubleshooting-guide.md): This document provides a general guide for troubleshooting when you encounter an error running an application (app) from the Tool Library.
- [Tips & tricks](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/tips-and-tricks.md)
- [Guide to analyzing large sample sets](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/tips-and-tricks/guide-to-analyzing-large-sample-sets.md)
- [Returning pVCF Files to UK Biobank](https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/returning-pvcf-files-to-uk-biobank.md): Learn how to prepare pVCF files and return them to UK Biobank.
- [About the science corner](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/about-the-science-corner.md): This section includes documentation on analyses that the DNAnexus team has performed to demonstrate how the scientific community can leverage the UKB-RAP.
- [End-to-end target discovery with GWAS and PheWAS](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/end-to-end-target-discovery-with-gwas-and-phewas.md)
- [Whole Exome Sequencing OQFE Protocol](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol.md)
- [Protocol for Processing UKB Whole Exome Sequencing Data Sets](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/protocol-for-processing-ukb-whole-exome-sequencing-data-sets.md)
- [Generation and Utilization of Quality Control Set 90pct10dp on OQFE Data](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/generation-and-utilization-of-quality-control-set-90pct10dp-on-oqfe-data.md)
- [Details on Processing Whole Exome Datasets to Generate the Quality Control Set](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/whole-exome-sequencing-oqfe-protocol/generation-and-utilization-of-quality-control-set-90pct10dp-on-oqfe-data/details-on-processing-the-300k-exome-data-to-generate-the-quality-control-set.md)
- [Burden testing with WES](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/burden-testing-with-wes.md)
- [GWAS guide using Alzheimer's disease](https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/gwas-using-alzheimers-disease.md): Explore one of the ways to conduct a GWAS on the Research Analysis Platform.