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github.com/TheJacksonLaboratory/LIRICAL @v2.4.1
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README
LIRICAL
LIRICAL (LIkelihood Ratio Interpretation of Clinical AbnormaLities) is designed to provide clinically interpretable computational analysis of phenotypic abnormalities (encoded using the Human Phenotype Ontology), optionally combined with an analysis of variants and genotypes if a VCF file is provided with the results of diagnostic gene panel, exome, or genome sequencing.
The prioritized diseases are reported in human-friendly HTML report. The report summarizes the most likely differential diagnoses:
and breaks down the contributions of the HPO terms and deleterious variants in the associated genes for each diagnosis:
The report is also available in JSON/TSV formats suitable for programmatic post-processing.
Availability
Most users should download the latest distribution ZIP file from the Releases page.
Learn more
Read more about the LIRICAL algorithm in the manuscript available at the American Journal of Human Genetics.
Consult the documentation for installation instructions and a tutorial: - Stable documentation - Edge release documentation
Developers can access API reference at: - Stable - Edge release
Extension points exported contracts — how you extend this code
SanitationInputs (Interface)The sanitation requirements. [6 implementers]
lirical-core/src/main/java/org/monarchinitiative/lirical/core/sanitize/SanitationInputs.java
PhenopacketImporter (Interface)
Decode phenopacket data from an input stream. [5 implementers]
lirical-io/src/main/java/org/monarchinitiative/lirical/io/analysis/PhenopacketImporter.java
PathogenicityScore (Interface)
@since 3.0.0 @author Jules Jacobsen [1 implementers]
lirical-exomiser-db-adapter/src/main/java/org/monarchinitiative/lirical/exomiser_db_adapter/model/pathogenicity/PathogenicityScore.java
AnalysisResultsWriter (Interface)
The implementors can store results of LIRICAL analysis in some OutputFormat. [4 implementers]
lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/AnalysisResultsWriter.java
VisualizableVariant (Interface)
The variant data for displaying in SVG widget. [1 implementers]
lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/VisualizableVariant.java
InputSanitizer (Interface)
Sanitize the user input before running the analysis. @author Daniel Danis [3 implementers]
lirical-core/src/main/java/org/monarchinitiative/lirical/core/sanitize/InputSanitizer.java
LiricalAnalysisRunner (Interface)
The analysis runner runs LIRICAL analysis on provided analysis subject (AnalysisData). The analysis is parametri [3 implementers]
lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/LiricalAnalysisRunner.java
SanitationResult (Interface)
Result of the input sanitation. The result consists of the inputs that were sanitized to the greatest extent possibl [2 …
lirical-core/src/main/java/org/monarchinitiative/lirical/core/sanitize/SanitationResult.java
Core symbols most depended-on inside this repo
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lirical-core/src/main/java/org/monarchinitiative/lirical/core/model/Gene2Genotype.java
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lirical-io/src/main/java/org/monarchinitiative/lirical/io/output/VisualizableVariant.java
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lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/AnalysisResults.java
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lirical-exomiser-db-adapter/src/main/java/org/monarchinitiative/lirical/exomiser_db_adapter/serializers/ProtobufDataType.java
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lirical-core/src/main/java/org/monarchinitiative/lirical/core/model/VariantMetadata.java
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lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/AnalysisResults.java
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lirical-exomiser-db-adapter/src/main/java/org/monarchinitiative/lirical/exomiser_db_adapter/model/pathogenicity/PathogenicityScore.java
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lirical-core/src/main/java/org/monarchinitiative/lirical/core/sanitize/SanityIssue.java
Shape
Languages
Java100%
Modules by API surface
lirical-exomiser-db-adapter/src/main/java/org/monarchinitiative/lirical/exomiser_db_adapter/model/frequency/FrequencyData.java41 symbols
lirical-core/src/main/java/org/monarchinitiative/lirical/core/output/AnalysisResultsMetadata.java39 symbols
lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/AnalysisOptions.java29 symbols
lirical-exomiser-db-adapter/src/main/java/org/monarchinitiative/lirical/exomiser_db_adapter/model/pathogenicity/ClinVarData.java24 symbols
lirical-core/src/main/java/org/monarchinitiative/lirical/core/analysis/TestResult.java22 symbols
lirical-io/src/main/java/org/monarchinitiative/lirical/io/analysis/PhenopacketData.java18 symbols
lirical-core/src/main/java/org/monarchinitiative/lirical/core/model/Age.java18 symbols
lirical-core/src/main/java/org/monarchinitiative/lirical/core/likelihoodratio/GenotypeLrWithExplanation.java18 symbols
lirical-io/src/main/java/org/monarchinitiative/lirical/io/LiricalDataResolver.java17 symbols
lirical-exomiser-db-adapter/src/main/java/org/monarchinitiative/lirical/exomiser_db_adapter/model/AlleleProtoAdaptor.java17 symbols
lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/cmd/LiricalConfigurationCommand.java17 symbols
lirical-cli/src/main/java/org/monarchinitiative/lirical/cli/yaml/YamlConfig.java16 symbols
For agents
$ claude mcp add LIRICAL \
-- python -m otcore.mcp_server <graph>