Uses of Class
biolockj.module.report.otu.OtuCountModule

Packages that use OtuCountModule

Package	Description
biolockj.module.report.otu
biolockj.module.report.taxa

Uses of OtuCountModule in biolockj.module.report.otu

Subclasses of OtuCountModule in biolockj.module.report.otu

Modifier and Type	Class and Description
class	CompileOtuCounts This BioModule compiles the counts from all OTU count files into a single summary OTU count file containing OTU counts for the entire dataset.
class	RarefyOtuCounts This BioModule applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.
class	RemoveLowOtuCounts This BioModule set low OTU counts below a configured threshold to zero. These low sample counts are assumed to be miscategorized or contaminents.
class	RemoveScarceOtuCounts This BioModule removes scarce OTUs not found in enough samples. The OTU must be found in a configurable percentage of samples.

Uses of OtuCountModule in biolockj.module.report.taxa

Subclasses of OtuCountModule in biolockj.module.report.taxa

Modifier and Type	Class and Description
class	BuildTaxaTables Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level.