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:
* David2014_: original microbiome dataset published in [David et al.,2014] (http://genomebiology.com/2014/15/7/R89)
* Ballou2016_: original microbiome dataset published in [Ballou et al.,2016] (http://journal.frontiersin.org/article/10.3389/fvets.2016.00002/full)
* Gajer2012_: original microbiome dataset published in [Gajer et al.,2012] (http://stm.sciencemag.org/content/4/132/132ra52.long)
* LaRosa2014_: original microbiome dataset published in [LaRosa et al.,2014] (http://www.pnas.org/cgi/doi/10.1073/pnas.1409497111)
* Dam2016_: original microbiome dataset published in [Dam et al.,2016] (https://www.nature.com/articles/npjsba20167)
* 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)
* Ravel2011_: original microbiome dataset published in [Ravel et al.,2011] (http://www.pnas.org/content/108/Supplement_1/4680)

Sufixes:
_All: all taxa
_Dominant: only 1% most abundant taxa
_NonDominant: remaining taxa after removing above dominant taxa
_GenusAll: taxa aggregated at genus level
_GenusDominant: taxa aggregated at genes level and then to select only 1% most abundant taxa
_GenusNonDominant: taxa aggregated at genus level and then to remove 1% most abundant taxa

Each folder contains the following output files related to the same input dataset:
- 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.
- definitiveClusteringResults_XXX.txt: text file with assessment measures of the selected clustering.
- sampleId-cluster_pairs_XXX.txt: text file. Two columns, comma separated file: sampleID,clusterID
- robustClustering_allTogether_formatted.pdf: graph file, with the results of the robust clustering assessment.
- pcoa_definitiveClustering_X_kY_colorByCluster.pdf: graph file, with samples represented in Principal COordinate Analysis, with different point color associated to the assigned cluster.
- statesSequence_XXX.pdf (if longitudinal data): graph file, a time series diagram representing the sequence of states over time per subject.