Tutorial purpose | Prerequisites | 1. Create a new project | 2. Print stored attributes about your project | 3. Get an existing project | Clean Up | References used in this tutorial

Tutorial purpose | Prerequisites | 1. Creating a table | Initial setup | Example data | Loading data | 2. Querying for data | 3. Changing Data | Appending new rows | Updating existing rows | Upserting (Update or Insert) rows | 4. Changing Table Structure | 5. Deleting Table Rows & Tables | Working with dates and datetimes | Storing timezone-aware datetimes (recommended) | Storing naive datetimes | Storing dates without a time of day | Loading date columns from a CSV | Querying datetime data back | Clean Up

Tutorial Purpose | Prerequisites | 1. Get the ID of your Synapse project | 2. Create your Dataset | 3. Add files to the dataset | 4. Retrieve the dataset | 5. Query the dataset | 6. Add a custom column to the dataset | 7. Save a snapshot of the dataset | References

Core Concepts | Access Control Lists (ACLs) | Benefactors and Inheritance | Permission Types | Special Principal IDs | Common Use Cases | Research Collaboration | Hierarchical Access Control | Data Governance | Best Practices | Security Considerations | Learn More | API References

Tutorial Purpose | Prerequisites | 1. Get the ID of your Synapse project | 2. Create your Dataset Collection | 3. Add Datasets to the Dataset Collection | 4. Retrieve the Dataset Collection | 5. Add a custom column to the Dataset Collection | 6. Query the Dataset Collection | 7. Save a snapshot of the Dataset Collection | References

Overview | Entity | Projects | Folders | Files | Annotations | Activity/Provenance

Tutorial Purpose | Prerequisites | 1. Build a mapping of Synapse IDs to download directories | 2. Download all files | References used in this tutorial

Tutorial Purpose | Prerequisites | 1. Download all files/folder from a project | First let's set up some constants we'll use in this script | Next we'll create an instance of the Project we are going to sync | Finally we'll sync the project from synapse to your local machine | 2. Control manifest CSV generation during download | 3. Download all files/folders for a specific folder within the project | 4. Loop over all files/folders on the project/folder object instances | References used in this tutorial

Tutorial purpose | Prerequisites | 1. Find the Synapse ID of your project | 2. Create an EntityView with Columns | 3. Query the EntityView | 4. Update rows in the EntityView | 5. Update the scope of your EntityView | 6. Update the types of Entities included in your EntityView | Results | References used in this tutorial

Tutorial purpose | Prerequisites | 1. Create and update an Evaluation on Synapse | 2. Update the ACL of an Evaluation on Synapse | 3. Retrieve and delete all Evaluations from a given Project | References

Overview | Prerequisites | 1. Upload several files to Synapse | First, retrieve the project and folders created in the Folders vignette | Next let's create all of the File objects to upload content | 2. Print stored attributes about your files | 3. List all Folders and Files within my project | Results | Clean Up | References used in this tutorial

Overview | Load the package and log in | Prerequisites | 1. Create a new folder | 2. Print stored attributes about your folder | 3. Create 2 sub-folders | Results | Clean Up | References used in this tutorial

Prerequisites | Install SynapseR from GitHub | A specific release, by its tag (for example, 2.1.5) | Install R | SynapseR Installation (WIP) | Install from RStudio | Install from R | Step-by-Step Installation with Dependency Management | Prerequisites: Verify Python Installation | R Installation Steps | Alternative Simple Installation | Troubleshooting | (Optional) Managing Python | Option 1: Using pyenv (Recommended) | Install pyenv | Configure pyenv | Install and set Python 3.10 | Option 2: Official Python Installer (Alternative)

Properties and annotations, implementation details | Properties and annotations are kept separate | Setting properties and annotations

Sharing Settings (ACL Management) in Synapse | Tutorial Purpose | Prerequisites | Understanding Permission Types | Special Principal IDs | Permission Inheritance and Benefactors | Benefactor Concept | Default Inheritance Behavior | Applying Permissions to Other Entities | 1. Set Up and Get Project | 2. Create a main folder to set custom sharing settings | 3. Examine Current Permissions | 4. Get ACL for Specific Principal | 5. Set Custom Permissions | 6. Create Sub-folder with Different Permissions | 7. List All ACLs | 8. Advanced Permission Management | 9. Remove Permissions | 10. Delete Entire ACLs | 11. Final Overview | Key Concepts Covered | Inheritance vs Local ACLs | Permission Management Functions | Best Practices | Common Use Cases | Research Collaboration | Data Sharing | Hierarchical Access | References used in this tutorial

Permissions Management | Project Structure | Top Level Folder Names | Flattened Data Layout Example | Hierarchy Data Layout Example | File Views | Creating the File View | Uploading annotations with manifests | An example: ELITE portal

What are Submissions? | Key Concepts | How Submissions Work | Related Objects | What You'll Learn | Tutorial Purpose | Prerequisites | 1. Participating in a Synapse challenge | Initial setup | 1. Make a submission to an existing evaluation queue on Synapse | 2. Fetch your existing submission | 3. Count your submissions | 4. Fetch all of your submissions from an existing evaluation queue on Synapse | 5. Check the status of your submission | 6. Cancel your submission | 2. Organizing a Synapse challenge | 1. Annotate a submission to score it | 2. Batch-update submission statuses | 3. Fetch the submission bundles for an evaluation queue | 4. Allow cancellation of submissions | 5. Delete submissions | References

Overview | Installation | Connecting to Synapse | Accessing Data | Organizing Data in a Project | Annotating Synapse Entities | Provenance | Tables | Wikis | Evaluations | Sharing Access to Content | File Views | Accessing the API Directly | Synapse Utilities | More information

Troubleshooting (WIP) | Build Synapser | Build Synapser when creating vignettes | Dependency Conflicts (rjson/reticulate) | Python Version Compatibility | R Version Compatibility | Troubleshooting R Version Issues: | Using Synapser with reticulate | Type Conversions | Poisoned cache and endswith error

Tutorial Purpose | Prerequisites | 1. Set up constants | 2. Create a manifest CSV file to upload data in bulk | 3. Upload the data in bulk | 4. Add an annotation to our manifest file | 5. Create an Activity/Provenance | References used in this tutorial

Tutorial purpose | Prerequisites | 1. Log in, get your project, and create tables with data | 2. Create and query a basic Virtual Table | 3. Create a Virtual Table with column selection | 4. Create a Virtual Table with filtering | 5. Create a Virtual Table with ordering | 6. Create a Virtual Table with aggregation | Clean Up | References

Overview | Prerequisites | 1. Create a Wiki page | Initial setup | 2. Update a Wiki page | 3. Restore a Wiki page to a previous version | 4. Get a Wiki page | 5. Create a sub-Wiki page | 6. Create a Wiki page from markdown | Create a Wiki page directly from a string | Create a Wiki page from a markdown file | 7. Download Wiki page markdown | Download the markdown file URL for a Wiki page | Download the markdown file for a Wiki page created from plain text | Download the markdown file for a Wiki page created from a markdown file | 8. Create Wiki pages with attachments | Create a Wiki page with attachments | 9. Retrieve attachment handles and URLs, and download attachments and previews | Get attachment handles | Get attachment URL without downloading | Download an attachment file | Get attachment preview URL | Download an attachment preview | 10. Retrieve Wiki page hierarchy using WikiHeader | 11. Access Wiki version history using WikiHistorySnapshot | 12. Get, set, and update Wiki page ordering using WikiOrderHint | Get the current order hint | Set the Wiki order hint | Update Wiki order hint | 13. Delete Wiki pages | Where to go next

Who this guide is for | Why upgrade now | Why this release is not backwards compatible | What you gain in 3.0 | Before you upgrade | Four patterns to relearn | 1. Instance-first, then pipe | 2. Properties are no longer nested under $properties and synSetProperties | 3. Arguments are snake_case, matching the Python client exactly | 4. Mutation goes through synSetProperties(), then an explicit synStore() | Side-by-side reference: common operations | Removed functions | Renamed or restructured | Not currently exposed in 3.0 | New in 3.0: capabilities that didn't exist before | Richer access control | Container traversal and sync | JSON Schema binding and validation | Known pitfall: integer literals | Worked example: before and after | Where to go next

Manifest file format | Required fields for upload | Standard fields | Metadata fields (ignored during upload) | Annotations | Multiple values of annotations per key | Dates in the manifest file | Manifest sources | Example manifest file | References

.synapseConfig sections | [default] and [profile ] | [sftp://hostname] | [https://s3.amazonaws.com/bucket_name] | [cache] | [debug] | [endpoints] | [transfer]

Overview | Key differences from the legacy API: | Load the package | Login | Create a Project | Create a Folder | Upload a File | Version the file | Add, Update and Remove Annotations | Add annotations to a file | Update annotations of a file | Remove annotations of a file | Download a File | Download a Specific Version | Clean Up

Prerequisites | One Time Login | Use .synapseConfig | Editing the ~/.synapseConfig file | Transitioning from One Profile to Multiple | Logging in with your ~/.synapseConfig file | Logging in via R | For more information, see:

Required System Dependencies | Python Version Requirements | Ubuntu Installation | Redhat Installation