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R Client for Seven Bridges Genomics API

The sbgr package provides an R client for accessing the Seven Bridges Genomics API.

Installation

The package is currently not availble in the Bioconductor release branch yet until next Bioc release cycle, please switch to the devel branch by following code to install.

source("http://bioconductor.org/biocLite.R")
useDevel(devel = TRUE)
biocLite("sbgr")

Alternatively, you can install the latest development version of the package from GitHub too:

# install.packages("devtools") if devtools was not installed
library("devtools")
install_github("road2stat/sbgr")

To load the package in R, simply call

library("sbgr")

Manual and Vignettes

Please check out the package page for more information, and two tutorials

© Seven Bridges Genomics 2012 - 2015. Licensed under the MIT license.

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Version

Version

1.0.0

License

MIT + file LICENSE

Maintainer

Nan Xiao

Last Published

February 15th, 2017

Functions in sbgr (1.0.0)

file_copy

Copy specified file(s) to the specified project
file_download_url

Returns a direct download URL for a project's file
Item-class

Class Item
file_details

Returns detailed information about a project's files
Auth-class

Class Auth
file_list

Returns the list of all project files for a project
billing

Returns the list of all billing groups you have access to
file_meta_update

Update project's file metadata
FileTypeSingleEnum-class

Metadata class
file_delete

Removes a file from a project
pipeline_list_project

Returns a list of all the pipelines in project
misc_upload_cli

Upload files using SBG uploader
pipeline_list_my

Returns the list of pipelines in user's "My Pipelines" section
project_delete

Delete a project
pipeline_add

Add a pipeline to a specified project
pipeline_details

Returns the details of a pipeline for a project
misc_make_metadata

Specify the parameters of the file metadata and return a list, JSON string, or write to a file
pipeline_list_pub

Returns the list of all public pipelines
misc_get_auth_token

Opens browser to copy the auth token
misc_get_uploader

Download SBG uploader and extract to a specified directory
project_list

Returns the list of all projects you have access to
project_details

Returns the details of the project
sbgr-package

R Client for Seven Bridges Genomics API
project_member_update

Set permissions for a user to a project
status_check

check request status
project_member_add

Add a user to the project with appropriate permissions
project_member_delete

Removes a member from a project
project_new

Create new project
project_members

Returns a list of all users invited to the project and their privileges
sbgapi

wrapper of http logic for SBG API
task_details

Returns information about the task
upload_delete

Aborts the upload
upload_complete_part

Reports the completion of the part upload
task_action

Performs action on the task
upload_complete_all

Reports the complete file upload
upload_info

Returns upload information for the ongoing upload
upload_info_part

Returns AWS S3 signed URL for a part of the file upload
Task-class

Task class
upload_init

Initializes the upload of the specified file
task_list

Returns the list of all the tasks for a project
task_run

Runs a task as a part of a project