All Classes
AddMetadataToPathwayTables
AddMetadataToTaxaTables
AwkFastaConverter
BashScriptBuilder
BioLockJ
BioLockJUtil
BioModule
BioModuleFactory
BioModuleImpl
BuildQiimeMapping
BuildTaxaTables
ClassifierModule
ClassifierModuleImpl
CompileOtuCounts
Config
ConfigException
ConfigFormatException
ConfigNotFoundException
ConfigPathException
ConfigViolationException
Constants
DatabaseModule
Demultiplexer
DemuxUtil
DockerUtil
DownloadUtil
Email
Gunzipper
Humann2Classifier
Humann2CountModule
Humann2Parser
ImportMetadata
JavaModule
JavaModuleImpl
JsonNode
JsonReport
KneadData
Kraken2Classifier
Kraken2Node
Kraken2Parser
KrakenClassifier
KrakenNode
KrakenParser
Log
LogTransformTaxaTables
LogUtil
MemoryUtil
MergeQiimeOtuTables
Metaphlan2Classifier
Metaphlan2Parser
MetaphlanNode
MetaUtil
ModuleUtil
Multiplexer
NextflowUtil
NormalizeTaxaTables
OtuCountModule
OtuNode
OtuNodeImpl
OtuUtil
OtuUtil.OtuCountLine
ParsedSample
ParserModule
ParserModuleImpl
PathwayUtil
PearMergeReads
Pipeline
Processor
Properties
PropUtil
QiimeClassifier
QiimeClosedRefClassifier
QiimeDeNovoClassifier
QiimeNode
QiimeOpenRefClassifier
QiimeParser
R_CalculateStats
R_Module
R_PlotEffectSize
R_PlotMds
R_PlotOtus
R_PlotPvalHistograms
RarefyOtuCounts
RarefySeqs
RdpClassifier
RdpNode
RdpParser
RegisterNumReads
RemoveLowOtuCounts
RemoveLowPathwayCounts
RemoveScarceOtuCounts
RemoveScarcePathwayCounts
RMetaUtil
RuntimeParamUtil
ScriptModule
ScriptModuleImpl
SeqFileValidator
SeqModule
SeqModuleImpl
SeqUtil
SummaryUtil
TaxaCountModule
TaxaUtil
TrimPrimers
UpdateJavaDocs