index.md

In nikopech/empdata: A 975-sample subset with 150-bp length sequences of the EMP (Earth Microbiome Project) dataset

empdata

This is a 975-sample subset of the EMP (Earth Microbiome Project) dataset containing 150bp-length sequences. All samples were picked randomly and evenly across 17 habitats and then evenly across 97 studies in each sample type.

This package provides the following data frames:

• biom_sub2k_150bp: observation-sequence counts per sample
• observation_metadata_sub2k150: observation-sequence taxonomy
• sample_metadata_sub2k: sample metadata

Installation

# install.packages("devtools")
devtools::install_github("nikopech/empdata")

Quick start

library(empdata)

str(biom_sub2k_150bp)
# str(observation_metadata_sub2k150)
# str(sample_metadata_sub2k)

License

All data sets were collected from the FTP site of the Earth Microbiome Project.

Sample processing, sequencing, and core amplicon data analysis were performed by the Earth Microbiome Project (www.earthmicrobiome.org), and all amplicon sequence data and metadata have been made public through the EMP data portal (qiita.microbio.me/emp).

Please cite the following publication if you use any of them:

Thompson, L., Sanders, J., McDonald, D. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017). https://doi.org/10.1038/nature24621

Please see the LICENSE file for details

nikopech/empdata documentation built on Oct. 13, 2021, 5:36 a.m.