api.rst

API Description

Study class

tmtk.Study

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Params classes

Params Container

tmtk.params.Params

Base class: ParamsBase

tmtk.params.ParamsBase

AnnotationParams

tmtk.params.AnnotationParams

ClinicalParams

tmtk.params.ClinicalParams

HighDimParams

tmtk.params.HighDimParams

StudyParams

tmtk.params.StudyParams

TagsParams

tmtk.params.TagsParams

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Clinical classes

Clinical Container

tmtk.clinical.Clinical

ColumnMapping

tmtk.clinical.ColumnMapping

DataFile

tmtk.clinical.DataFile

Variable

tmtk.clinical.Variable

WordMapping

tmtk.clinical.WordMapping

Annotations

Annotations Container

tmtk.annotation.Annotations

Base class: AnnotationBase

tmtk.annotation.AnnotationBase

ChromosomalRegions

tmtk.annotation.ChromosomalRegions

MicroarrayAnnotation

tmtk.annotation.MicroarrayAnnotation

MirnaAnnotation

tmtk.annotation.MirnaAnnotation

ProteomicsAnnotation

tmtk.annotation.ProteomicsAnnotation

High Dimensional data

HighDim

tmtk.highdim.HighDim

HighDimBase

tmtk.highdim.HighDimBase

CopyNumberVariation

tmtk.highdim.CopyNumberVariation

Expression

tmtk.highdim.Expression

Mirna

tmtk.highdim.Mirna

Proteomics

tmtk.highdim.Proteomics

ReadCounts

tmtk.highdim.ReadCounts

SampleMapping

tmtk.highdim.SampleMapping

Metadata Tags

Tags

tmtk.tags.Tags

Utilities

FileBase

tmtk.utils.filebase

Generic module

tmtk.utils.Generic

utils.CPrint module

tmtk.utils.CPrint

utils.Exceptions module

tmtk.utils.Exceptions

utils.HighDimUtils module

tmtk.utils.HighDimUtils

utils.mappings module

tmtk.utils.mappings

Toolbox package

Generate chromosomal regions file

tmtk.toolbox.generate_chromosomal_regions_file

Remap chromosomal regions data

tmtk.toolbox.remap_chromosomal_regions

Study Wizard

tmtk.toolbox.wizard

Create study from templates

tmtk.toolbox.create_study_from_templates

The Arborist

tmtk.arborist.common module

tmtk.arborist.common

tmtk.arborist.connect_to_baas module

tmtk.arborist.connect_to_baas

tmtk.arborist.jstreecontrol module

tmtk.arborist.jstreecontrol