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. Thanks to Valentina Giunchiglia for the curation of these additional datasets.

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_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.