Data From: Robust And Automatic Definition Of Microbiome States

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.