Uses of Package
org.monarchinitiative.lirical.core.analysis

Packages that use org.monarchinitiative.lirical.core.analysis

Package	Description
org.monarchinitiative.lirical.cli.cmd	Commands to run LIRICAL in different configurations.
org.monarchinitiative.lirical.core	Core functionality of the LIRICAL algorithm.
org.monarchinitiative.lirical.core.analysis	A high-level representation of LIRICAL analysis.
org.monarchinitiative.lirical.core.analysis.impl	Default LIRICAL analysis implementation.
org.monarchinitiative.lirical.core.output	Base data model for writing out the results of LIRICAL analysis.
org.monarchinitiative.lirical.io.analysis	Read user input formatted as a v1 or v2 phenopacket.
org.monarchinitiative.lirical.io.output	Classes for writing out LIRICAL analysis results into HTML, TSV, and JSON files.
org.monarchinitiative.lirical.io.output.svg	Classes to create an SVG graphic representing the result of likelihood raio analysis of one HPO Case.

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.cli.cmd

Class	Description
LiricalParseException	An exception thrown when user-provided input is invalid.

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.core

Class	Description
LiricalAnalysisRunner	The analysis runner runs LIRICAL analysis on provided analysis subject (AnalysisData).

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.core.analysis

Class	Description
AnalysisData	Representation of subject data required by LIRICAL analysis.
AnalysisOptions	A container for analysis-specific settings, i.e.
AnalysisOptions.Builder	A builder for AnalysisOptions.
AnalysisResults	A container for the likelihood ratio test results.
LiricalAnalysisException	An exception thrown by LiricalAnalysisRunner if the analysis cannot be run.
TestResult	This class organizes information about the result of a test.

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.core.analysis.impl

Class	Description
AnalysisData	Representation of subject data required by LIRICAL analysis.
AnalysisOptions	A container for analysis-specific settings, i.e.
AnalysisResults	A container for the likelihood ratio test results.
LiricalAnalysisException	An exception thrown by LiricalAnalysisRunner if the analysis cannot be run.
LiricalAnalysisRunner	The analysis runner runs LIRICAL analysis on provided analysis subject (AnalysisData).

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.core.output

Class	Description
AnalysisData	Representation of subject data required by LIRICAL analysis.
AnalysisResults	A container for the likelihood ratio test results.

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.io.analysis

Class	Description
LiricalParseException	An exception thrown when user-provided input is invalid.

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.io.output

Class	Description
AnalysisData	Representation of subject data required by LIRICAL analysis.
AnalysisResults	A container for the likelihood ratio test results.
TestResult	This class organizes information about the result of a test.

Classes in org.monarchinitiative.lirical.core.analysis used by org.monarchinitiative.lirical.io.output.svg

Class	Description
AnalysisResults	A container for the likelihood ratio test results.
TestResult	This class organizes information about the result of a test.