Package: sevenbridges 1.43.0

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