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{laminr}: An R client for LaminDB

CRAN status Lifecycle: experimental R-CMD-check

{laminr} is an R package that provides an interface to LaminDB.

Warning

This package is currently in early access and is under active development. Features, APIs, and functionality are subject to change.

What is LaminDB

If you are new to LaminDB, it's helpful to start with Lamin's problem statement. LaminDB is an open-source data framework for biology, built as a Python API that structures data and metadata, tracks analysis lineage, and enables reproducible, scalable research. With tools for curating data against public ontologies and flexible dataset querying, LaminDB is designed to address core data challenges in the field. Please refer to LaminDB's introduction for a more detailed introduction. LaminDB is accompanied by LaminHub which is a data collaboration hub built on LaminDB similar to how Github is built on git.

Features of {laminr}

  • Connect to a LaminDB instance and list all records in a registry.
  • Fetch records by ID or UID.
  • Cache artifacts locally.
    • Currently supported storage backends: s3.
    • Planned: gcs.
  • Load artifacts into memory.
    • Currently supported file formats: .csv, .h5ad, .html, .jpg, .json, .parquet, .png, .rds, .svg, .tsv, .yaml.
    • Planned: .fcs, .h5mu, .zarr.
  • Create records from data frames, paths and AnnData objects.
  • Delete records.
  • Track code in R scripts and notebooks.

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):

  • Getting 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")).

Learn more

For more information about LaminDB and its features, check out the following resources: