In waldronlab/MicrobiomeBenchmarkData: Datasets for benchmarking in microbiome research

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## This code is to import the description of the datasets
## Only the table should be displayed on the vignette
library(MicrobiomeBenchmarkData)
fname <- system.file(
    'extdata/datasets.tsv', package = 'MicrobiomeBenchmarkData'
)
datasets <- read.table(
    fname, header = TRUE, sep = '\t', check.names = FALSE
)
data('sampleMetadata', package = 'MicrobiomeBenchmarkData')
PMID <- dplyr::distinct(
    sampleMetadata[, c('dataset', 'pmid')]
)
datasets <- dplyr::left_join(datasets, PMID, by = c('Dataset' = 'dataset'))
datasets <- dplyr::rename(datasets, PMID = pmid)

In the table below, you can find the collection of datasets currently available through the MicrobiomeBenchmarkData package. These datasets are also avialable on Zenodo: https://doi.org/10.5281/zenodo.6911026

## Show table
knitr::kable(datasets, filter = 'top')

sessionInfo()

waldronlab/MicrobiomeBenchmarkData documentation built on May 2, 2024, 1:20 p.m.