Package ubic.gemma.apps
@ParametersAreNonnullByDefault
package ubic.gemma.apps
This package contains built-in Gemma CLI applications.
For third-party applications, use ubic.gemma.contrib.apps instead.
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ClassesClassDescriptionAdd (or possibly replace) the data associated with an affymetrix data set, going back to the CEL files.Purely a testing tool, to turn Affy individual probes (by probeset) into collapsed sequences.This only needs to be re-run when the mappings change.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.work in progressRemove all associations that this array design has with BioSequences.Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB.CLI for ArrayDesignMapSummaryServicemake 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.Delete design elements (probes) that are invalid for one reason or another.Process the blat results for an array design to map them onto genes.Deprecated.renaming probes is not a good idea in generalRuns repeatmasker on array designs.Attach sequences to array design, fetching from BLAST database if requested.Aggregates functionality useful when writing CLIs that need to get an array design from the database and do something with it.Test two array designs to see if one subsumes the other, and if so update their information.For bulk processing of batch-info-fetching.Refreshes the information in all the bibliographic references in the system.Goes through the biosequences for array designs in the database and removes duplicates.Add entries to the blacklistThis CLI provide various runtime completions that can be re-used by other CLIs.Simple driver of DatabaseViewGenerator.Delete differential expression analsyes on a per-experiment basis.Delete one or more experiments from the system.A command line interface to the
DifferentialExpressionAnalysis.Writes differential expression analysis files to disk.Writes out the experimental design for a given experiment.Create correlation visualizations for expression experimentsPrints preferred data matrix to a file.Deprecated.useDifferentialExpressionAnalysisWriterCliinstead.Update GEO data for an experiment.Base class for CLIs that needs one or more expression experiment as an input.CLI tool for adding manual entries to the changelog file of an experiment.CLI tool for viewing the changelog file of an experiment.Add a metadata file to an experiment and record an entry in the changelog file.Switch the array design used to the merged one.Update the primary publication for experiments.Base class for CLI tools that manipulate expression experiment vectors.Add a new external database, but requires editing the code to do so.CLI for loading genes from a non NCBI files.Deprecated.this will be removed as soon as all the old-style characteristics are migratedGenerate or update GEEQ scoresGenerate a database update script.Create (or update) an array design based on a list of NCBI gene IDs desired to be on the platform.Scans GEO for experiments that are not in Gemma, subject to some filtering criteria, outputs to a file for further screening.Initialize the database.Commandline tool to conduct link (coexpression) analysis.List all locks within Gemma's data directories.Simple command line to load expression experiments, either singly or in batches defined on the command line or in a file.Command Line tools for loading the expression experiment in flat filesThis CLI allows one to lock an experiment data or metadata file.Make data sets public.Deprecated.should not be part of Gemma main codeLoad GO -> gene associations from NCBI.Command line interface to gene parsing and loadingUse to change the order of the values to match the experimental design.Prepare the "processed" expression data vectors, and can also do batch correction.Load PubMed files from XML files -- not used routinely!Simple application to perform pubmed searches from a list of terms, and persist the results in the database.Replace data in an existing data set.Deprecated.this should not be necessary and the regular batch population tool can be used instead.Designed to add count and/or RPKM data to a data set that has only meta-data.Transform various single-cell formats.Split an experiment into parts based on an experimental factorUpdate the database.Identify experiments in Gemma that have no publication Fetch their GEO records and check for pubmed IDs Add the publications where we find them.For experiments that used multiple array designs, merge the expression profiles