Uses of Class
ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

Packages that use ArrayDesignSequenceManipulatingCli

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.

Uses of ArrayDesignSequenceManipulatingCli in ubic.gemma.apps

Subclasses of ArrayDesignSequenceManipulatingCli in ubic.gemma.apps

Modifier and Type	Class	Description
class	AffyProbeCollapseCli	Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.
class	ArrayDesignAnnotationFileCli	Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or merged into another AD.
class	ArrayDesignAuditTrailCleanupCli	work in progress
class	ArrayDesignBioSequenceDetachCli	Remove all associations that this array design has with BioSequences.
class	ArrayDesignBlatCli	Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.
class	ArrayDesignMapSummaryCli	CLI for ArrayDesignMapSummaryService
class	ArrayDesignMergeCli	make new array design based on others Keep map of relation between new design elements and old ones Store relationship with mergees Separate operations: For an EE, Remap DesignElement references to old array designs to new one, and old BioAssay AD refs to new one.
class	ArrayDesignProbeCleanupCLI	Delete design elements (probes) that are invalid for one reason or another.
class	ArrayDesignProbeMapperCli	Process the blat results for an array design to map them onto genes.
class	ArrayDesignProbeRenamerCli	Deprecated. renaming probes is not a good idea in general
class	ArrayDesignRepeatScanCli	Runs repeatmasker on array designs.
class	ArrayDesignSequenceAssociationCli	Attach sequences to array design, fetching from BLAST database if requested.
class	ArrayDesignSubsumptionTesterCli	Test two array designs to see if one subsumes the other, and if so update their information.
class	BioSequenceCleanupCli	Goes through the biosequences for array designs in the database and removes duplicates.