cMD

curatedMetagenomicData



Curated and processed metagenomic data through ExperimentHub

Ongoing datasets

Shown below is a list of forthcoming datasets that have been chosen for inclusion in curatedMetagenomicData.

Dataset Name PMID Publication Year Bodysite Disease Number of Samples
BarnardE_2016 28000755 2016 Skin Acne 78
GeveresD_2014 24629344 2014 Stool CD 50
HMP_phaseII     Several Other condition 1200
HMP2     Several IBD, T2D 3528
HuangAD_2016 27881416 2016 Stool Other condition 10
KorpelaK_2016 26811868 2016 Stool Other condition 256
KosticAD_2015 25662751 2015 Stool T1D 124
LiJ_2014 24997786 2014 Stool Other condition 260
LiJ_2017 28143587 2017 Stool Hypertension 196
LiSS_2016 27126044 2016 Stool Other condition 430
LuisS_2016 26919743 2016 Stool Obesity 92
ManorO_2016 26940651 2016 Stool Cystic fibrosis 104
MilaniC_2016 27166072 2016 Stool CDI 15
MurphyR_2016 27738970 2016 Stool T2D 28
Nagy-SzakalD_2017 28441964 2017 Stool ME/CFS 100
OhJ_2016 27153496 2016 Skin Other condition 406
OlmMR_2017 28073918 2017 Stool, skin, oral Other condition 45
PehrssonEC_2016 27172044 2016 Stool Other condition 116
PiperHG_2016 27406942 2016 Stool SBS 11
QuinceC_2015 26526081 2015 Stool IBD 117
RoseG_2017 5270596 2017 Stool Other condition 15
ScherJU_2013 24192039 2013 Stool Other condition 44
TremaroliV_2015 26244932 2016 Stool Other condition 21
VoigtAY_2015 25888008 2015 Stool Other condition 70
YassourM_2016 27306663 2016 Stool Other condition 240
ZeeviD_2015 26590418 2015 Stool Other condition 1523
ZehernakovaA_2016 27126040 2016 Stool Other condition 1135
ZhangX_2015 26214836 2015 Stool Rheumatoid arthritis 202

Authors welcome the addition of new metagenomic datasets provided that the raw data are hosted by NCBI/SRA and can be run through our MetaPhlAn2 and HUMAnN2 pipeline. You can request the addition of a dataset by opening an issue on the issue tracker, pointing us to the publication and raw data.