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_pkgdown.yml
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url: https://bhklab.github.io/AnnotationGx/
template:
bootstrap: 5
development:
mode: auto
#####################################################################
# References for functions
#####################################################################
reference:
- title: Dataset Metadata
subtitle: CCLE
contents:
- CCLE_sampleMetadata
- CCLE_treatmentMetadata
- subtitle: GDSC
contents:
- GDSC_sampleMetadata
- GDSC_treatmentMetadata
- subtitle: CTRP
contents:
- CTRP_sampleMetadata
- CTRP_treatmentMetadata
- subtitle: gCSI
contents:
- gCSI_sampleMetadata
- gCSI_treatmentMetadata
- title: ID Cleaning
subtitle: ID Cleaning
contents:
- cleanCharacterStrings
- standardize_names
- title: Cellosaurus
subtitle: API query
contents:
- cellosaurusAPIVersion
- cellosaurus_fields
- mapCell2Accession
- annotateCellAccession
- title: PubChem
subtitle: REST API query
contents:
- getPubchemCompound
- mapCompound2CID
- mapCID2Properties
- getPubchemProperties
- getPubchemStatus
- subtitle: VIEW API query
contents:
- getPubchemAnnotationHeadings
- annotatePubchemCompound
- title: UniChem
subtitle: REST API query
contents:
- getUnichemSources
- queryUnichemCompound
- title: ChEMBL
subtitle: REST API query
contents:
- queryChemblAPI
- getChemblMechanism
- getChemblResourceFields
- getChemblResources
- getChemblFilterTypes
- title: OncoTree
subtitle: API query
contents:
- getOncotreeVersions
- getOncotreeMainTypes
- getOncotreeTumorTypes
- title: CancerTargetDiscoveryDevelopment (CTD2)
subtitle: API query
contents:
- mapCompound2CTD
- title: Utility Functions
contents:
- strSplit
- unlistNested
- matchNested
#####################################################################
# Articles
#####################################################################
articles:
- title: Introduction
navbar: Introduction
contents:
- Introduction
- title: Samples
navbar: Annotating Samples
contents:
- Cellosaurus
- OncoTree
- title: Compounds
navbar: Annotating Compounds
contents:
- PubChemAPI
- Unichem
- ChEMBL
- title: Pipelines
navbar: Pipeline Tutorials
contents:
- articles/AnnotationStandards
- articles/CTRP-Treatment-Annotation