05. Download data

Download data from microbiomedatarepo

We have made few trial datasets available for beginners. These data are part of the meta-analysis paper from Claire Duvallet et al. 2017 Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. A lot of effort was made by Claire Duvallet et al. 2017 to curate the data and we thank them. For example of reading mothur we use the data from Baxter et al., 2014 Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions. We also acknowledge Baxter et al., for making the data publicly available.

library(microbiomeutilities)

# check the dataset list
list_microbiome_data()

[1] "data from Duvallet et al 2017 https://www.nature.com/articles/s41467-017-01973-8.pdf?origin=ppub"
1] Schubert et al., CDI 336 samples [cdi_schubert.rds]
2] Youngster et al., CDI 23 samples [cdi_youngster.rds]
3] Goodrich et al., OB 613 samples [ob_goodrich.rds]
4] Dinh et al., HIV 36 samples [hiv_dinh.rds]
5] Zeller et al., CRC 116 samples [crc_zeller.rds]
6] example of mothur file from Baxter et al., 2016 
 i) baxter_shared.shared 
 ii) baxter_con.taxonomy 
 iii) baxter_metadat.csv

We will download the Youngster et al. data.

ps1 <- get_microbiome_data(studynumber = 2)

print(ps1)