All Classes
AddMetadataToPathwayTables
AddMetadataToTaxaTables
AddPseudoCount
API_Exception
ApiModule
AwkFastaConverter
BashScriptBuilder
BasicDockerMapper
BioLockJ
BioLockJ_API
BioLockJException
BioLockJStatusException
BioLockJUtil
BioModule
BioModuleFactory
BioModuleImpl
BuildDocs
BuildQiimeMapping
BuildTaxaTables
ClassifierModule
ClassifierModuleImpl
CommonDockerMapper
CompileOtuCounts
Config
ConfigConflictException
ConfigException
ConfigFormatException
ConfigNotFoundException
ConfigPathException
ConfigViolationException
Constants
DatabaseModule
Demultiplexer
DemuxUtil
DESeq2
DirectModuleException
DockerImageException
DockerLaunchProcess
DockerMountMapper
DockerUtil
DockerVolCreationException
DockerVolumeException
DownloadUtil
EdgeR
Email
EndLaunch
ExpectationFileFormatException
FatalExceptionHandler
FileWithoutMetadataException
ForEachFile
ForEachLevel
ForEachLoop
ForEachSample
GenMod
GenomeAssembly
Gunzipper
Hello_Friends
Hello_World
Humann2Classifier
Humann2CountModule
Humann2Parser
ImportMetadata
InputDataModule
IntentionalStop
InvalidPipelineException
JavaLaunchProcess
JavaModule
JavaModuleImpl
JsonNode
JsonReport
KneadData
Kraken2Classifier
Kraken2Node
Kraken2Parser
KrakenClassifier
KrakenNode
KrakenParser
LabeledSpinner
Launcher
LaunchProcess
Log
LogTransformTaxaTables
LogUtil
MasterConfigUtil
MemoryUtil
MergeQiimeOtuTables
MetadataException
MetadataWithoutFileException
Metaphlan2Classifier
Metaphlan2Parser
MetaphlanNode
MetaUtil
ModuleUtil
Multiplexer
NextflowUtil
NormalizeByReadsPerMillion
NormalizeTaxaTables
OtherPipeline
OtherPipelineFactory
OtherPipelineImpl
OtuCountModule
OtuFileException
OtuNode
OtuNodeImpl
OtuUtil
OtuUtil.OtuCountLine
OutsidePipelineWriter
ParsedSample
ParserModule
ParserModuleImpl
PathMapper
PathwayUtil
PearMergeReads
Pipeline
PipelineFormationException
PipelineScriptException
PipelineUtil
Processor
ProgressMsgDemo
ProgressUtil
Properties
QiimeClassifier
QiimeClosedRefClassifier
QiimeDeNovoClassifier
QiimeNode
QiimeOpenRefClassifier
QiimeParser
R_CalculateStats
R_Module
R_PlotEffectSize
R_PlotMds
R_PlotOtus
R_PlotPvalHistograms
RarefyOtuCounts
RarefySeqs
RdpClassifier
RdpHierParser
RdpNode
RdpParser
ReadCounter
RegisterNumReads
RemoveLowOtuCounts
RemoveLowPathwayCounts
RemoveScarceOtuCounts
RemoveScarcePathwayCounts
RequiredRPackageException
Reset
Rmarkdown
RMetaUtil
RuntimeParamException
RuntimeParamUtil
ScriptModule
ScriptModuleImpl
SeqFileValidator
SeqModule
SeqModuleImpl
SequenceReadArchive
SequnceFormatException
SeqUtil
ShannonDiversity
SimpleDockerMapper
SpecialPropertiesException
SraDownload
SraMetaData
SraMetaDB
SrpSrrConverter
Step1
Step2
Step3
Step4
Step5
Stop
StopAfterPrecheck
StopModuleException
SummaryUtil
TaxaCountModule
TaxaLevelTable
TaxaUtil
TransformTaxaTables
TrimPrimers
UpdateJavaDocs
ValidationException
ValidationExecutionException
ValidationUtil
ValidationUtilityException