{"doi":"10.1101/103085","title":"Accessible, curated metagenomic data through ExperimentHub","abstract":"We present curatedMetagenomicData, a Bioconductor and command-line interface to thousands of metagenomic profiles from the Human Microbiome Project and other publicly available datasets, and ExperimentHub, a platform for convenient cloud-based distribution of data to the R desktop. The resource provides standardized per-participant metadata linked to bacterial, fungal, archaeal, and viral taxonomic abundances, as well as quantitative metabolic functional profiles. The datasets can be immediately analyzed in R or other software with a minimum of bioinformatic expertise and no preprocessing of data. We demonstrate identification of taxonomic/functional correlations, an investigation of gut “enterotypes”, and a comparison of the accuracy of disease classification from different data types. These documented analyses can be reproduced efficiently on a laptop, without the barriers of working with large-scale, raw sequencing data. The building and expansion of curatedMetagenomicData is based entirely on open source software and pipelines, to facilitate the addition of new microbiome datasets and methods.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2017,"id":5827,"datarank":2.048315452494413,"base_score":4.189654742026425,"endowment":4.189654742026425,"self_citation_contribution":0.6284482113039639,"citation_network_contribution":1.4198672411904492,"self_endowment_contribution":0.6284482113039639,"citer_contribution":1.4198672411904492,"corpus_percentile":89.54900595652511,"corpus_rank":1352,"citation_count":65,"citer_count":56,"citers_with_citation_signal":41,"citers_with_endowment":41,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9408,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2017-01-27","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":56065,"name":"Lucas Schiffer","orcid":"0000-0003-3628-0326","position":1,"is_corresponding":false},{"id":56066,"name":"Paolo Manghi","orcid":"0000-0003-0846-6529","position":2,"is_corresponding":false},{"id":36302,"name":"Audrey Renson","orcid":"0000-0003-1603-2587","position":3,"is_corresponding":false},{"id":56067,"name":"Valerie Obenchain","orcid":null,"position":4,"is_corresponding":false},{"id":56068,"name":"Duy Tin Truong","orcid":"0000-0002-4169-7727","position":5,"is_corresponding":false},{"id":36315,"name":"Francesco Beghini","orcid":"0000-0002-8105-9607","position":6,"is_corresponding":false},{"id":56069,"name":"Faizan Malik","orcid":"0000-0001-8597-5074","position":7,"is_corresponding":false},{"id":11437,"name":"Marcel Ramos","orcid":"0000-0002-3242-0582","position":8,"is_corresponding":false},{"id":36375,"name":"Jennifer B. Dowd","orcid":"0000-0003-2006-5656","position":9,"is_corresponding":false},{"id":493,"name":"Curtis Huttenhower","orcid":"0000-0002-1110-0096","position":10,"is_corresponding":false},{"id":56070,"name":"Martin Morgan","orcid":"0000-0002-5874-8148","position":11,"is_corresponding":false},{"id":29160,"name":"Alyxandria M. Schubert","orcid":"0000-0003-4938-6007","position":12,"is_corresponding":false},{"id":489,"name":"Levi Waldron","orcid":"0000-0003-2725-0694","position":13,"is_corresponding":false},{"id":36346,"name":"Edoardo Pasolli","orcid":"0000-0003-0799-3490","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"green","license":"cc-by-nc","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}