Home

Jump to bottom

James Masanz edited this page Oct 26, 2018 · 20 revisions

Cancer Deep Phenotype Extraction (DeepPhe)

Getting started

See the introduction to the DeepPhe system.

Open the Pages section (above) to view all pages by title.

Installation
   Windows
   Mac
   Linux
   Known Issues

Quickstart
   Windows Quickstart Tutorial
   Mac Quickstart Tutorial
   Command line-execution

Using DeepPhe-XN With Your Own Files
   Input File Requirements
   Configuring DeepPhe Phenotype Summarizer
   Specifying and Interpreting Outputs

Example Files Description
   Using DeepPhe-XN Visualizer
   Additional Output File Types
   Example File Data Specifics

About the DeepPhe Pipeline
Pipeline Description

Code Modules

AE
division
- BiomarkerFinderNew
- GeneFinder
- GleasonFinderNew
- GradeFinderNew
- HistologyFinder
- StageFinder
- TopographyFinder
section
- CrSectionizer
- PittHeaderAnnotator
- SectionRemover
- Sectionizer
- WtfSectionFixer
temporal
- DoubledEventRemover
BiomarkerFinder
CancerAttributeAdjuster
ClockFaceFinder
CrRelationFinder
DiseaseAttributeFinder
DistancedRemover
DistinctValueFinder
DocEpisodeTagger
GleasonFinder
GradeFinder
GraphRelationFinder
HistoryAdjuster
InDocUriRelationFinder
JsonNodeCreator
Ki67Finder
LonerNegator
MassFilter
MelanomaDocEpisodeTagger
NonGraphedRelationFinder
PatientNodeCollector
PatientSummaryCleaner
PipelineStopper
PsaFinder
SectionIdSetter
SubjectAdjuster
TnmFinderAe
CR
filetree
- NaaccrDirHandler
- NaaccrFileHandler
- NaaccrXmlReader
naaccr
- AbstractNaaccrItem
- InfoItemType
- NaaccrDocument
- NaaccrItem
- NaaccrItemGetter
- NaaccrItemType
- NaaccrPatient
- NaaccrSection
- NaaccrSectionGetter
- NaaccrSectionType
- NaaccrTumor
- NaaccrXmlFile
- RegistryXmlHandler
- RegistryXmlReader
Hl7Reader

Licensing
Funding
Contact / Help

Wiki Conventions

Clone this wiki locally