Overview | Why are elevated permissions required? | Supported backends | Opal | Required permissions | Configuring an Opal audit user | Step 1: Log in as an administrator | Step 2: Create a user (optional) | Step 3: Grant audit permissions | Example usage | Troubleshooting | Insufficient permissions | Testing Opal permissions directly

What is Opal? | Deploy Docker containers | Setup | Open connection | Test deployment

1. Creating your first RO-Crate | 1.1. Connect to an Opal server | Open connection | 1.2. Create a basic RO-Crate | 1.3. Add the Five Safes Elements | Safe Data | Safe Project | Safe People | Safe Setting | Safe Outputs | DataSHIELD operations | Setup | Simulate some operations | 1.4. Close connection | 1.5. Bag/Save RO-Crate | 1.6. Clean working directory | 2. Auditing RO-Crates and servers | 2.1. Audit People | List accessible tables within a project for an user | Markdown report | 2.2. Audit Project | List users and dataset/table level permissions within a project | 2.3. Audit Study | List users and dataset/table level permissions within a study (i.e., multiple servers)

Introduction | What is an RO-Crate? | RO-Crate Structure | 1. Functions Overview | 2. First RO-Crate | 3. Including additional entities | 4. Wrangle RO-Crate | 4.1. Set up | 4.2. Extract entity | 4.2.1. Extract using @id | 4.2.2. Extract using @type | 4.2.3. Extract using @id and @type | 4.3. Remove entity | 4.3.1. Remove using scalar @id | 4.3.2. Remove using entity object | 4.3.3. Remove multiple entities | 5. Create an RO-Crate Bag | 5.1. rocrateR::bag_rocrate() | 5.2. rocrateR::is_rocrate_bag() | 5.3. rocrateR::unbag_rocrate() | 6. Validation | Appendix | A1. Advanced Validation (experimental) | A1.1. Install | A1.2. Install rocrate-validator | A1.3. Create example RO-Crate and validate it