Package edu.cmu.cs.sb.drem

Class Summary
DREM_DataSet Class extends DataSetCore which contains the underlying data and parameters of the methods with an instance of DREM_GoAnnotations
DREM_FastLogistic2 Class implements a logistic regression classifier trained with an L1 penalty.
DREM_GoAnnotations Class encapsules the Gene Ontology annotations and gene set enrichment functions used by DREM
DREM_GoAnnotations.RecIDdrem A record for a GO category include ID, name, p-value based on a split, and a p-value overall
DREM_GoAnnotations.RecIDdremCompare Compares first by dpvalue (lower comes first) and then by dcategoryselect (greater comes first)
DREM_IO Class implementing the main input interface
DREM_NaiveBayes Implements a naive bayes classifier This class is used for predicting whether a gene with a specified set of regulators will be filtered or not.
DREM_Timeiohmm This class implements the core methods for learning the DREM maps
DREMGui Class for the main interface window of a DREM regulatory map
DREMGui_DefineGeneSet Class for the window used to directly specify a subset of genes to select
DREMGui_EdgeTable Class for a table that shows enrichment of TF targets along a path
DREMGui_FilterGOModel Class implements a table model, which is used for the define gene set table
DREMGui_FilterStatic Class encapsulates window used to select a subset of genes based on the static transcription factors in the input to regulate the gene.
DREMGui_FilterStaticModel Class implements a table model, which is used for selected genes based on static input
DREMGui_GeneTable Class encapsulates a gene table which is used to display the selected genes in DREM
DREMGui_GOFilter Class encapsulates window used to select a subset of genes all belonging to the same GO category
DREMGui_GOGeneTable Class encapsulates a table of genes all assigned to the same GO category when clicking on a GO category in a GOTable
DREMGui_GOSplitTable Encapsulates a table providing information on GO enrichments for the sets of genes on paths out of splits conditioned on the set of genes going into the split
DREMGui_GOTable Class that encapsulates a GO Enrichment table in DREM
DREMGui_ImageFilter Class used to specify the file filtering in the file chooser menu.
DREMGui_InterfaceOptions Class encapsulates the interface option window for the main interface
DREMGui_KeyInputs Class encapsulates the window used to specify the criteria that determines transcription factor labels appear on the main interface
DREMGui_Predict Class encapsulates a window to specify an input for each transcription factor, then displays a probability of transitioning to each hidden state
DREMGui_PredictModel Class implements a table model, which is used for the prediction interface
DREMGui_SaveDREM Class for window to specify to save the current DREM main interface as an image
DREMGui_SaveModel Class to encapsulate window used to specify a file to save a DREM model
DREMGui_SplitTable Class encapsulating a table showing enrichment of gene targets of transcription factors out of splits
DREMGui_StaticSummaryTable Class for a table summarizing the TF-gene enrichments for a selected set of gene This is the table that comes up when pressing the TF summary button
DREMGui.SigInfoRec Record for information about significant transcription factors