Uses of Class
ubic.gemma.cli.util.AbstractAutoSeekingCLI
Packages that use AbstractAutoSeekingCLI
-
Uses of AbstractAutoSeekingCLI in ubic.gemma.apps
Subclasses of AbstractAutoSeekingCLI in ubic.gemma.appsModifier and TypeClassDescriptionclassAdd (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.classGiven 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.classwork in progressclassRemove all associations that this array design has with BioSequences.classCommand line interface to run blat on the sequences for a microarray; the results are persisted in the DB.classCLI for ArrayDesignMapSummaryServiceclassmake 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.classDelete design elements (probes) that are invalid for one reason or another.classProcess the blat results for an array design to map them onto genes.classDeprecated.renaming probes is not a good idea in generalclassRuns repeatmasker on array designs.classAttach sequences to array design, fetching from BLAST database if requested.classAggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.classTest two array designs to see if one subsumes the other, and if so update their information.classFor bulk processing of batch-info-fetching.classGoes through the biosequences for array designs in the database and removes duplicates.classclassDelete differential expression analsyes on a per-experiment basis.classDelete one or more experiments from the system.classclassA command line interface to theDifferentialExpressionAnalysis.classWrites differential expression analysis files to disk.classclassWrites out the experimental design for a given experiment.classCreate correlation visualizations for expression experimentsclassPrints preferred data matrix to a file.classDeprecated.useDifferentialExpressionAnalysisWriterCliinstead.classUpdate GEO data for an experiment.classBase class for CLIs that needs one or more expression experiment as an input.classCLI tool for adding manual entries to the changelog file of an experiment.classCLI tool for viewing the changelog file of an experiment.classAdd a metadata file to an experiment and record an entry in the changelog file.classSwitch the array design used to the merged one.classUpdate the primary publication for experiments.classBase class for CLI tools that manipulate expression experiment vectors.classGenerate or update GEEQ scoresclassCommandline tool to conduct link (coexpression) analysis.classclassThis CLI allows one to lock an experiment data or metadata file.classclassMake data sets public.classUse to change the order of the values to match the experimental design.classPrepare the "processed" expression data vectors, and can also do batch correction.classclassclassclassclassReplace data in an existing data set.classDeprecated.this should not be necessary and the regular batch population tool can be used instead.classDesigned to add count and/or RPKM data to a data set that has only meta-data.classclassclassclassclassclassclassSplit an experiment into parts based on an experimental factorclassclassclassclassFor experiments that used multiple array designs, merge the expression profiles