Package org.systemsbiology.inference

This package contains classes used to infer the set of elements affected by a perturbation of a biological system, based on multiple evidences.

See:
Description

Class Summary

DataManagerDriver	A graphical tool for merging ObservationsData data files.
DataNormalizationMethod	Species how the DataNormalizer should normalize a matrix of raw observations.
DataNormalizationScale	Specifies the scale to be used for the DataNormalizer.
DataNormalizer	Performs a normalization of a matrix of raw observations, so that each column of the matrix is consistent, based on the DataNormalizationMethod passed in the DataNormalizerParams object.
DataNormalizerDriver	A graphical user interface for normalizing raw observations using the DataNormalizer.
DataNormalizerParams	Describes how the DataNormalizer is to normalize the data.
DataNormalizerResults	The results of a call to the DataNormalizer.
EvidenceWeightedInferer	An implementation of the Pointillist algorithm for inferring the set elements affected by a perturbation of a biological system, based on multiple types of evidence.
EvidenceWeightedInfererDriver	Graphical user interface for the Pointillist algorithm for inferring the set of elements affected by a perturbation of a biological system.
EvidenceWeightedInfererParams	Data structure that holds the parameters that are passed to the EvidenceWeightedInferer, to describe how the Pointillist algorithm should run.
EvidenceWeightedInfererResults	A data structure that holds the results of a call to the EvidenceWeightedInferer.
EvidenceWeightType	Enumerates the formulas that may be used for computing the evidence-specific weights.
ObservationsData	A data structure containing a set of observations for M elements, and N types of evidence.
ObservationsTableModel	A graphical user interface table model for ObservationsData.
PreferencesHandler	Gets and sets user preferences for the org.systemsbiology.inference package GUI programs.
SignificanceCalculationMethod	Enumerates the possible formulas for computing the significance of an observation, based on the distribution of "negative control" observations.
SignificanceCalculationResults	Data structure containing the results of a call to the SignificanceCalculator.
SignificanceCalculator	Based on a set of "negative control" observations, computes the significance of each of a set of observations.
SignificanceCalculatorDriver	Graphical user interface for calling the SignificanceCalculator to obtain significances of observations.
SignificanceCalculatorParams	The set of parameters that are passed to the SignificanceCalculator, describing how the significance calculation should be performed.
SignificancesData	Contains a matrix of significance values of a set of observations for M elements and N evidence types.

Package org.systemsbiology.inference Description

This package contains classes used to infer the set of elements affected by a perturbation of a biological system, based on multiple evidences.