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 |