Unofficial R Interface to the "Benchling Cloud R&D" Laboratory Information Management System (LIMS).
Benchling is a laboratory information management system (LIMS) with a developer platform that is comprised of a Postgres database, an application programming interface (API), an "Events" system that is built on top of the AWS EventBridge service, as well as a Python software development kit (SDK).
benchlingr is an unofficial R package that streamlines common data science and engineering operations by providing functions to extract and join tables in the Benchling data warehouse, download file attachments, extract tables from notebook entries, and upload assay results to the Benchling platform.
Install the R package directly from GitHub using the install_github function in the remotes package. Use install.packages('remotes') to install the remotes package if you do not already have it and see the documentation with ?remotes::install_github for more information.
remotes::install_github("hemoshear/benchlingr")
The full documentation is at: https://benchling-r.info
Please use GitHub issues for questions, feature requests, and bug reports. If you are submitting a bug report, please include the output of sessioninfo::session_info(), as well as your code to help us understand the problem.
The benchlingr package uses the RESTFUL API and Postgres database components of the Benchling developer platform. In order to access the API and database, one must acquire API keys and database credentials through the Benchling interface. This section will focus on how to make these credentials available to the benchlingr package.
Note: If you are unable to generate an API key and/or database credentials, you may need to ask your Benchling administrator for developer access
In order to access the Benchling API service on one's Benchling tenant, one must obtain an API key through the Benchling interface.. After obtaining an API key, it is recommended that you define a variable in .Renviron called BENCHLING_API_KEY to make this key accessible to the benchlingr package, since functions in the package will look for BENCHLING_API_KEY by default.
# ~/.Renviron
# Benchling API key
BENCHLING_API_KEY=xxxxxxxxxxx
Follow the instructions in the official documentation to obtain a username and password for the data warehouse for your Benchling tenant. After obtaining a username and password, it is recommended that one define a variable in .Renviron called BENCHLING_WAREHOUSE_KEY and BENCHLING_WAREHOUSE_PASSWORD to make the credentials available to benchlingr with the default settings.
# ~/.Renviron
# Benchling API key
BENCHLING_API_KEY=xxxxxxxxxxx
# Benchling warehouse credentials
BENCHLING_WAREHOUSE_USERNAME=yyyyyyyyyyy
BENCHLING_WAREHOUSE_PASSWORD=xxxxxxxxxxx
See the contribution guidelines for more information.