VPMBench
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Table of Contents
VPMBench - A test bench for variant prioritization methods
Installation
Core Concepts
Quickstart
Experimental Features
Developer Interface
VPMBench
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Index
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Index
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A
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B
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C
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D
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E
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F
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I
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L
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M
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N
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P
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R
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S
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V
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W
_
_extract() (vpmbench.extractor.Extractor method)
_extract_pathogencity_class_from_record() (vpmbench.extractor.VCFExtractor method)
_row_to_evaluation_data_entry() (vpmbench.extractor.CSVExtractor method)
_validate_score_table() (vpmbench.plugin.Plugin static method)
A
Accuracy (class in vpmbench.metrics)
AnnotatedVariantData (class in vpmbench.data)
AreaUnderTheCurveROC (class in vpmbench.metrics)
B
build_plugin() (vpmbench.plugin.PluginBuilder class method)
C
calculate() (vpmbench.metrics.Accuracy static method)
(vpmbench.metrics.Concordance static method)
(vpmbench.metrics.MatthewsCorrelationCoefficient static method)
(vpmbench.metrics.NegativePredictiveValue static method)
(vpmbench.metrics.Precision static method)
(vpmbench.metrics.Sensitivity static method)
(vpmbench.metrics.Specificity static method)
(vpmbench.summaries.ConfusionMatrix static method)
(vpmbench.summaries.PrecisionRecallCurve static method)
(vpmbench.summaries.ROCCurve static method)
calculate_metric_or_summary() (in module vpmbench.api)
calculate_metrics_and_summaries() (in module vpmbench.api)
ClinVarVCFExtractor (class in vpmbench.extractor)
Concordance (class in vpmbench.metrics)
ConfusionMatrix (class in vpmbench.summaries)
CSVExtractor (class in vpmbench.extractor)
cutoff (vpmbench.plugin.Score property)
D
DEFAULT_PLUGIN_PATH (in module vpmbench.config)
DockerEntryPoint (class in vpmbench.plugin)
E
EntryPoint (class in vpmbench.plugin)
EvaluationData (class in vpmbench.data)
EvaluationDataEntry (class in vpmbench.data)
extract() (vpmbench.extractor.Extractor method)
extract_evaluation_data() (in module vpmbench.api)
Extractor (class in vpmbench.extractor)
F
format_input() (in module vpmbench.processors)
format_output() (in module vpmbench.processors)
from_records() (vpmbench.data.EvaluationData static method)
from_results() (vpmbench.data.AnnotatedVariantData static method)
I
interpret() (vpmbench.plugin.Score method)
interpreted_classes (vpmbench.data.EvaluationData property)
invoke_method() (in module vpmbench.api)
invoke_methods() (in module vpmbench.api)
is_compatible_with_data() (vpmbench.plugin.Plugin method)
is_multiclass_plugin() (in module vpmbench.predicates)
L
load_plugin() (in module vpmbench.api)
load_plugins() (in module vpmbench.api)
M
MatthewsCorrelationCoefficient (class in vpmbench.metrics)
module
vpmbench.api
vpmbench.config
vpmbench.data
vpmbench.enums
vpmbench.extractor
vpmbench.metrics
vpmbench.plugin
vpmbench.predicates
vpmbench.processors
vpmbench.summaries
vpmbench.utils
N
NegativePredictiveValue (class in vpmbench.metrics)
P
PerformanceMetric (class in vpmbench.metrics)
PerformanceSummary (class in vpmbench.summaries)
plot_confusion_matrices() (in module vpmbench.utils)
plot_precision_recall_curves() (in module vpmbench.utils)
plot_roc_curves() (in module vpmbench.utils)
Plugin (class in vpmbench.plugin)
PluginBuilder (class in vpmbench.plugin)
Precision (class in vpmbench.metrics)
PrecisionRecallCurve (class in vpmbench.summaries)
PythonEntryPoint (class in vpmbench.plugin)
R
ReferenceGenome (class in vpmbench.enums)
report_metrics() (in module vpmbench.utils)
resolve() (vpmbench.enums.ReferenceGenome static method)
(vpmbench.enums.VariationType static method)
ROCCurve (class in vpmbench.summaries)
run() (vpmbench.plugin.DockerEntryPoint method)
(vpmbench.plugin.EntryPoint method)
(vpmbench.plugin.Plugin method)
(vpmbench.plugin.PythonEntryPoint method)
S
Score (class in vpmbench.plugin)
score_column_name (vpmbench.plugin.Plugin property)
scores (vpmbench.data.AnnotatedVariantData property)
Sensitivity (class in vpmbench.metrics)
Specificity (class in vpmbench.metrics)
V
validate() (vpmbench.data.EvaluationData method)
variant_data (vpmbench.data.EvaluationData property)
VariationType (class in vpmbench.enums)
VariSNPExtractor (class in vpmbench.extractor)
VCFExtractor (class in vpmbench.extractor)
vpmbench.api
module
vpmbench.config
module
vpmbench.data
module
vpmbench.enums
module
vpmbench.extractor
module
vpmbench.metrics
module
vpmbench.plugin
module
vpmbench.predicates
module
vpmbench.processors
module
vpmbench.summaries
module
vpmbench.utils
module
W
was_trained_with() (in module vpmbench.predicates)
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