AAbAtlas

R client for the antibodyome-atlas, a curated catalog of autoantibody profiling datasets and papers. See schema/README.md in the atlas repo for the data model.

Install

install.packages("AAbAtlas", repos = "https://ahcm088.r-universe.dev")

r-universe rebuilds automatically on every change to this package, so this always tracks the latest source. Not yet on CRAN. To install straight from a specific commit/branch instead:

# install.packages("pak")
pak::pak("ahcm088/antibodyome-atlas/r-package")

Usage

library(AAbAtlas)

# browse
ds <- aab_datasets()
ds[ds$record_type == "DATASET" & ds$total_sample_n > 100, c("atlas_id", "title", "total_sample_n")]

# one record, with its publication and platforms resolved
rec <- aab_dataset("AAB-000004")
rec$title
rec$publication$citation

# citation ready to paste into a manuscript
aab_citation("AAB-000004")

# download the underlying file
aab_download("AAB-000004")

By default every function reads the latest curated data (ref = "main"). Pin a release tag for reproducibility in a publication:

aab_datasets(ref = "v1.0.0")