- dataStr - Static variable in class peridot.CLI.AnalysisFileParser
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- defaultBuilderOperations(File, File, Spreadsheet.Info, String, int) - Method in class peridot.AnalysisData
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- defaultDBs - Static variable in class peridot.Organism
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The list of default ID types.
- defaultIDTypes - Static variable in class peridot.GeneIdType
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The list of default ID types.
- defaultInterpreter - Variable in class peridot.Archiver.PeridotConfig
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- defaultInterpreter - Static variable in class peridot.script.r.Interpreter
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- defaultModulesDir - Static variable in class peridot.Archiver.Places
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The directory where the defaults module, that can be loaded to modulesDir, are stored.
- defaultRportableDirs() - Static method in class peridot.Archiver.Places
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- defineAvailableParamTypes() - Static method in class peridot.script.RModule
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- defineCmdNameAndDetails() - Method in class peridot.CLI.Command
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- defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.IN
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- defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.LS
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- defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.OUT
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- defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.R
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- defineCmdNameAndDetails() - Method in class peridot.CLI.Commands.RUN
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- defineCommand(Interpreter) - Method in class peridot.script.r.Script
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- defineCommand() - Method in class peridot.script.ScriptRunnable
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- defineIsRunningRunnable() - Method in class peridot.script.ScriptExec
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- defineStatusWatcher() - Method in class peridot.script.Task
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- defineZombieFinder() - Method in class peridot.script.Task
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- deletePeridotFolder() - Static method in class peridot.Global
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Delete the whole r-peridot-files folder.
- deleteScript(String) - Static method in class peridot.script.RModule
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- detail - Variable in class peridot.CLI.Command
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- detectPreviousRunn() - Method in class peridot.script.ScriptRunnable
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- DiffExpressionModule - Class in peridot.script
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- DiffExpressionModule(String, String, boolean, boolean) - Constructor for class peridot.script.DiffExpressionModule
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- DiffExpressionModule(File) - Constructor for class peridot.script.DiffExpressionModule
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- dirExists(String) - Static method in class peridot.Archiver.Manager
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Checks for the existence of a directory.