{laminr}: An R client for LaminDB

{laminr} is an R client for LaminDB. If you are new to LaminDB, please read this introduction.

• Connect to a LaminDB instance: db <- connect()
• Track scripts and notebooks as transforms: db$track()
• Get records by UID: artifact <- db$Artifact$get()
• Cache artifacts locally: artifact$cache()
• Load artifacts into memory for a broad range of storage formats: artifact$load()
• Create artifacts from data frames, paths, and AnnData objects: db$Artifact$from_path()
• Delete records: artifact$delete()

See the development roadmap for more details (vignette("development", package = "laminr")).

Installation

Get started with {laminr} by installing the package from CRAN:

install.packages("laminr")

You will also need to install the lamindb Python package:

pip install lamindb[aws]

Additional packages

Some functionality requires additional packages. To install all of these use:

install.packages("laminr", dependencies = TRUE)

This will also install these package for the following tasks:

• {anndata} - Native AnnData support in R
• {nanoparquet} - Reading .parquet files
• {readr} - Reading CSV/TSV files
• {reticulate} - Functionality that requires the Python lamindb package
• {rsvg} - Reading SVG files
• {s3} - Fetching datasets from AWS S3

If you choose not to install all packages now you will be prompted to do so whenever one is required.

Getting started

The best way to get started with {laminr} is to explore the package vignettes (available at laminr.lamin.ai):

• Get started: Learn the basics and explore practical examples (vignette("laminr", package = "laminr")).
• Package Architecture: Get a better understanding of how {laminr} works (vignette("architecture", package = "laminr")).

For information on specific modules and functionalities, check out the following vignettes:

• Core Module: Learn about the core registries available in a LaminDB instance (vignette("module_core", package = "laminr")).
• Bionty Module: Explore the bionty module for biology-related entities (vignette("module_bionty", package = "laminr")).