Authentication | Direct authentication | Authentication via system environment variables | Authentication via user configuration file | API general information | Advance Access Features | Query Parameter fields | Rate Limits | General API error handlers | List All API Calls | Users | Billing Groups and Invoices | Billing groups | Invoices | Send a feedback item

File upload | Upload single file | Upload fields and operations | Print upload job | File size, part size and part number/length | Start upload | Get status information about the job | List all ongoing uploads | Abort upload process | Volumes | List volumes | Get single volume information | Create volumes - AWS (S3) using IAM User authentication type | Volume object operations | Update volume | Reload volume | List volume's content | Volume files and prefixes | Get VolumeFile info | Reload VolumeFile object | Get VolumePrefix info | List volume members | Remove members | Adding new members | Users with ADMIN privileges on divisions or enterprises | Modifying a member's permissions | Deactivate and reactivate the volume | Delete volume | Imports | List volume imports | Get a single import job | Get bulk import jobs | Submit new import - import a volume file into the project | Reload import job | Submit bulk import - import multiple volume files or folders into a project | Exports | List file exports to the volumes | Get a single export job | Get bulk export jobs | Submit a new export - export a file from the platform to a volume | Reload export job | Submit bulk export - export multiple files into a volume

Introduction | R Client for the Seven Bridges API | Installation | API General Information | Quickstart | Create Auth Object | Get User Information | Rate Limit | Show Billing Information | List and query projects | Create a new project | Get details of a specified project | Copy app into the project | Execute a new task | Find your app inputs | Prepare your input files | Create a new draft task | Preview your app's expected outputs | Run a Task | Run tasks using spot instances | Execution hints per task run | Draft a batch task

Managing Divisions | List all your divisions | Get details of a division | List all your teams in a division | List members of a division | Remove a member from a division | Managing teams | Team object methods | Listing team members | Adding a member to a team | Removing a team member | Renaming a team | Deleting a team

Projects | List all projects | Partial match project name | Filter by project creation date, modification date, and creator | Create a new project | Get a single project | Delete a project | Edit an existing project | Project members management | List project members | Add a member to a project | Get and modify a project member's permissions | Remove a project member | List project files | Create a folder within project Files | Get a project's root folder object | List project's apps, tasks and import jobs | Create a new app and task within a project | Files, folders and metadata | List files | List public data | Get a single file/folder | Delete a file | Asynchronous delete action on multiple files/folders | Copy files | Asynchronous bulk copy of multiple files | Get details of multiple files | Update details of multiple files | Edit details of multiple files | Get details of all asynchronous file jobs | Create a folder within the destination project or parent folder | Asynchronous bulk move of multiple files | File object operations | File print | Update file details | Add tags to a file | Copy a single file between projects | Get downloadable URL for a file | Get a file's metadata | Modify file metadata | List folder contents | Move a file into a folder | Download a file | Get a file's parent directory | Delete a file/folder | Delete multiple files/folders | Reload a file | Apps | List apps | List project apps | Get app information | Copy an app | Create new app | Create an app in a project | App object operations | Print an app | Get an app's raw CWL | Preview app's inputs and expected outputs | Get an app revision | Create an app revision | Sync a copied app | Reload an app | Tasks | List tasks | Get single task information | Get details of multiple tasks | Create a draft task | Create a batch task | Task operations | Print task | Run a task | Abort a task | Clone a task | Get execution details | List batch children | Update task | Rerun a task | Reload task | Delete task

Introduction | R Client for Seven Bridges API | API General Information | Installation | Quickstart | Create Auth Object | Get User Information | Rate Limit | Show Billing Information | Create Project | Get Details about Existing Project | Copy Public Apps into Your Project | Import CWL App and Run a Task | Execute a New Task | Find your app inputs | Get your input files ready | Create a new draft task | Draft a batch task | Run a Task | Run tasks using spot instances | Execution hints per task run | Task Monitoring | Seven Bridges API Reference | Authentication | Direct authentication | Authentication via system environment variables | Authentication via user configuration file | List All API Calls | Offset, Limit, Search, and Advance Access Features | offset and limit | Search by ID | Search by name | Experiment with Advance Access features | Query Parameter 'fields' | Rate Limits | Users | Billing Group and Invoices | For billing | For invoices | Project | List all projects | Partial match project name | Filter by project creation date, modification date, and creator | Create a new project | Create a new project with TCGA controlled data on CGC | Delete a project | Update/edit a project | Project member | List members | Add a member | Update a member | Delete a member | List all files | Files, Metadata, and Tags | Search and filter file(s) | Rule of thumb | Search by name and id | Search by metadata | Search by tags | Search by original task id | Copy a file or group of files | Delete file(s) | Download files | Upload files via API | Upload single file | Upload a folder | Upload a list of files | Upload files via a defined manifest file | Upload files via command line uploader | Update a file | Metadata operations | Tag file(s) | Folders | Get project root folder | Create a folder | Copy files between folders | Move files between folders | List folder contents | Get file and folder details | Delete files in a folder | Delete a folder | Apps | List all apps | Copy an app | Get an app's CWL description | Add CWL as an app | Describe CWL in R directly | Create test or keep the previous test for Tool | Tasks | List tasks | Create a draft task | Modify a task | Run a task | Abort a running task | Delete a task | Download all files from a completed task | Run tasks in batch mode | Download all files from a batch task | Volumes | Create a volume | List and search all volumes | Get a volume's detail | Delete volume | Import file from volume to project | Export file from project to volume | Public Files and Apps | Public files | Public apps | Actions | Copy files between projects | Send a feedback item | Enterprise | API token for the division context | List all divisions | Get details of a division | Create a team | Get details of a team | Add a team member | List team members | Remove a team member | Rename a team | List your teams in the division | Delete a team | Markers | Create a marker | List markers available on a file | Get details for a marker | Modify a marker | Delete a marker | Get Raw Response from httr | Batch Operation on Project/Files/Tasks | API Cheatsheet

Prerequisite | Apps, Workflows, and Tools | Describe Tools in R | Import from JSON file | Utilitites for Tool object | Create your own tool in R | Introduction | Using existing Docker images and command | Add customized script to existing Docker image | Create formal interface for your command line | Quick command line interface with commandArgs (position and named args) | docopt: a better and formal way to make command line interface | Generate reports | Misc | Describe Wokrflow in R | Import from a JSON file | Utilities for Flow objects | Create your own flow in R | Connect simple linear tools | Connecting tools by input and output id | Connecting tool with workflow by input and output id | Using pipe to construct complicated workflow | Execution | Execute the tool and flow in the cloud | Execute the tool in Rabix -- test locally

Introduction | Existing Docker repos | Rocker Project | Bioconductor Images | Docker Hub | Seven Bridges Docker Registry | Tutorial: Random Number Generator | Using docopt Package | Quick Command Line Interface with commandArgs (Position and Named Args) | Quick Report: Spin and Stich | Executable Report with R Markdown (Advanced) | Setup Docker Hub Automated Build | More Examples

Introdution | Graphical Data Browser | Datasets API | Browse TCGA via the Datasets API | Return datasets accessible trough the CGC | Return list of all TCGA entities | Interpreting the list of all entities | Copy files to you project | Post with query | Find samples connected to a case | Find cases with given age at diagnosis | Find cases with a given age at diagnosis and disease | Complex example for filtering TCGA data | Query with multiple filters on a case

Introduction | Docker container | Build container locally | Pull from Docker Hub | Launch RStudio Server from Docker container | Launch both RStudio Server and Shiny Server from the same Docker container

Introduction | Prerequisites | Installation | Register on Cancer Genomics Cloud | Authentication | Register on shinyapps.io (Optional) | Report issues | Quickstart | Create a project under your account via API R client | Build a RNA-Seq tool: from bam to report | Step 1: Have a plan | Step 2: Create Docker container for your tool | Step 3: Create your command line interface | Step 4: Add default report template to your app | Step 5: Describe your tool in R into CWL | Step 6: Execute your tool with a new task via R API | Build a reporting Tool | What is report tool? | Compose a full workflow | Exercise: bring your own tool | More tutorials