{"doi":"10.5281/zenodo.1485915","title":"Data From: Robust And Automatic Definition Of Microbiome States","abstract":"Output files of the application of our R software (available at https://github.com/wilkinsonlab/robust-clustering-metagenomics) to different microbiome dataset already published. Prefixes:<br> * David2014_: original microbiome dataset published in [David et al.,2014] (http://genomebiology.com/2014/15/7/R89)<br> * Ballou2016_: original microbiome dataset published in [Ballou et al.,2016] (http://journal.frontiersin.org/article/10.3389/fvets.2016.00002/full)<br> * Gajer2012_: original microbiome dataset published in [Gajer et al.,2012] (http://stm.sciencemag.org/content/4/132/132ra52.long)<br> * LaRosa2014_: original microbiome dataset published in [LaRosa et al.,2014] (http://www.pnas.org/cgi/doi/10.1073/pnas.1409497111)<br> * Dam2016_: original microbiome dataset published in [Dam et al.,2016] (https://www.nature.com/articles/npjsba20167)<br> * Caporaso[Lpalm|Rpalm|Tongue]_: original microbiome dataset published in [Caporaso et al.,2011] (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-5-r50)<br> * Ravel2011_: original microbiome dataset published in [Ravel et al.,2011] (http://www.pnas.org/content/108/Supplement_1/4680) Sufixes:<br> _All: all taxa<br> _Dominant: only 1% most abundant taxa<br> _NonDominant: remaining taxa after removing above dominant taxa<br> _GenusAll: taxa aggregated at genus level<br> _GenusDominant: taxa aggregated at genes level and then to select only 1% most abundant taxa<br> _GenusNonDominant: taxa aggregated at genus level and then to remove 1% most abundant taxa <br> Each folder contains the following output files related to the same input dataset:<br> - data.normAndDist_definitiveClustering_XXX.RData: R data file with a) a phyloseq object (including OTU table, meta-data and cluster assigned to each sample); and b) a distance matrix object.<br> - definitiveClusteringResults_XXX.txt: text file with assessment measures of the selected clustering.<br> - sampleId-cluster_pairs_XXX.txt: text file. Two columns, comma separated file: sampleID,clusterID<br> - robustClustering_allTogether_formatted.pdf: graph file, with the results of the robust clustering assessment.<br> - pcoa_definitiveClustering_X_kY_colorByCluster.pdf: graph file, with samples represented in Principal COordinate Analysis, with different point color associated to the assigned cluster.<br> - statesSequence_XXX.pdf (if longitudinal data): graph file, a time series diagram representing the sequence of states over time per subject.","journal":"Zenodo (CERN European Organization for Nuclear Research)","year":2018,"id":6302,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10355,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9501,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":2,"downloads":386,"has_version_chain":false,"published_date":"2018-11-13","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":606,"name":"Mark D D. Wilkinson","orcid":"0000-0001-6960-357X","position":1,"is_corresponding":false},{"id":1680,"name":"Beatriz García-Jiménez","orcid":"0000-0002-8129-6506","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"citation_network_status":"fetched"},"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","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":[]}