cMD

curatedMetagenomicData



Curated and processed metagenomic data through ExperimentHub

Included datasets

Shown below is the list of datasets currently included in the development version of curatedMetagenomicData. Not all are available in the release version. To run the development version, you must upgrade to the development version of Bionductor. Simply installing the most recent curatedMetagenomicData from GitHub won’t work without the corresponding development version of ExperimentHub, and the easiest way to accomplish this is by upgrading your full Bioconductor installation.

Dataset Name PMID Publication Year Bodysite Disease Number of Samples
AsnicarF_2017 28144631 2017 Stool, milk None 24
BritoIL_2016 27409808 2016 Stool, oral Other condition 312
Castro-NallarE_2015 26336637 2015 Oral Schizophrenia 32
ChngKR_2016 27562258 2016 Skin Atopic dermatitis 78
FengQ_2015 25758642 2015 Stool CRC 154
HanniganGD_2017 - - Stool CRC 82
Heitz-BuschartA_2016 27723761 2016 Stool T1D 53
HMP_2012 22699609 2012 Several None 749
KarlssonFH_2013 23719380 2013 Stool T2D 145
LeChatelierE_2013 23985870 2013 Stool Obesity 292
LiJ_2014 24997786 2014 Stool Other condition 260
LiuW_2016 27708392 2016 Stool Other condition 110
LomanNJ_2013 23571589 2013 Stool STEC 43
NielsenHB_2014 24997787 2014 Stool IBD 396
Obregon-TitoAJ_2015 25807110 2015 Stool Other condition 58
OhJ_2014 25279917 2014 Skin None 291
QinJ_2012 23023125 2012 Stool T2D 363
QinN_2014 25079328 2014 Stool Cirrhosis 237
RampelliS_2015 25981789 2015 Stool Other condition 38
RaymondF_2016 26359913 2016 Stool Other condition 72
SchirmerM_2016 27984736 2016 Stool None 471
TettAJ_2016 28649415 2017 Skin Psoriasis 97
VatanenT_2016 27259157 2016 Stool Other condition 785
VincentC_2016 26975510 2016 Stool CDI 229
VogtmannE_2016 27171425 2016 Stool CRC 110
XieH_2016 27818083 2016 Stool Other condition 250
YuJ_2015 26408641 2015 Stool CRC 128
ZellerG_2014 25432777 2014 Stool CRC 199

The figure shows datasets ordered from lowest to highest median read depth, with boxes colored by body site.