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Multi-locus datasets are created from individual alignments that do not have "too many" missing entries using a bipartite graph of taxa and loci and combining with bicliques or quasi-bicliques [ 22, 23].
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21 datasets were created from the screening data.
Datasets were created from PubChem confirmatory BioAssay [AID-492952 (replicating), and AID-488890 (non-replicating)] screens of drug tolerant M.tb H37Rv in carbon starvation model [20, 21].
Initially, three datasets were created from the complete dataset.
B = 1,000 bootstrap datasets were created from each of the 4,000 RI1 datasets by sampling with replacement until n = 200 individual observations were obtained.
To validate the performance of FARO in a more quantitative fashion, two benchmarking datasets were created from the Rosetta compendium of yeast gene expression profiles [4].
The first 100 bootstrapped datasets were created from the original Cytb dataset with the program Mesquite v. 2.01 [ 78].
Fifteen datasets were created from 1 to 15 TM segments (the number of available proteins with more TMs is too small for this assessment).
Similarly, two GSEA-formatted datasets were created from the Illumina expression data: the first dataset compares the two phenotypes (WT +R5020 versus WT -R5020), and the second compares the two phenotypes (KR +R5020 versus KR -R5020).
A parametric dataset was created from DIFF by setting the signal in voxels belonging to Cl3 and Cl4 to zero.
By using Network Analyst extension tool in ArcMap application of ArcGIS, new road network dataset was created from the error-free road shapefile.
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