Package index • AnnotationGx

Dataset Metadata

CCLE

CCLE_sampleMetadata: CCLE_sampleMetadata is some preprocessed sample metadata from the CCLE dataset

CCLE_treatmentMetadata: CCLE_treatmentMetadata is some preprocessed treatment metadata from the CCLE dataset

GDSC

GDSC_sampleMetadata: gdsc_sampleMetadata is some preprocessed sample metadata from the GDSC dataset

GDSC_treatmentMetadata: GDSC_treatmentMetadata is some preprocessed treatment metadata from the GDSC dataset

CTRP

CTRP_sampleMetadata: CTRP_sampleMetadata is some preprocessed sample metadata from the CTRP dataset

CTRP_treatmentMetadata: CTRP_treatmentMetadata is some preprocessed treatment metadata from the CTRP dataset

gCSI

gCSI_sampleMetadata: gCSI_sampleMetadata is some preprocessed sample metadata from the gCSI dataset

gCSI_treatmentMetadata: gCSI_treatmentMetadata is some preprocessed treatment metadata from the gCSI dataset

ID Cleaning

ID Cleaning

cleanCharacterStrings(): Clean character strings by removing special characters and formatting.

standardize_names(): Standardize Names

Cellosaurus

API query

cellosaurusAPIVersion(): Get the Cellosaurus API version

cellosaurus_fields(): Get the list of fields in the Cellosaurus schema

mapCell2Accession(): Map Cell Line IDs to Accession Numbers

annotateCellAccession(): Annotate Cell Accession

PubChem

REST API query

getPubchemCompound(): Retrieve PubChem compound information

mapCompound2CID(): Map compound names to PubChem CIDs

mapCID2Properties(): Map PubChem Compound IDs to Properties

getPubchemProperties(): Retrieves the PubChem XML schema and extracts property information.

getPubchemStatus(): Retrieves the status of a PubChem request

VIEW API query

getPubchemAnnotationHeadings(): Get annotation headings (name only) based on type and heading criteria.

annotatePubchemCompound(): Annotate PubChem Compound

UniChem

REST API query

getUnichemSources(): Get the list of sources in UniChem.

queryUnichemCompound(): Query UniChem for a compound.

ChEMBL

REST API query

queryChemblAPI(): Query the ChEMBL API

getChemblMechanism(): Get ChEMBL Mechanism

getChemblResourceFields(): Get the fields of a Chembl resource

getChemblResources(): getChemblResources function

getChemblFilterTypes(): Get the Chembl filter types

OncoTree

API query

getOncotreeVersions(): Get available Oncotree versions

getOncotreeMainTypes(): Get the main types from the Oncotree database.

getOncotreeTumorTypes(): Get the tumor types from the Oncotree database.

HGNC Gene Symbols

API query

query_hgnc_by_genes(): Query HGNC BioMart by Gene Symbols

Utility Functions

strSplit(): Split a character vector into a matrix based on a delimiter

unlistNested(): Unlists a nested list and removes NA values and duplicates.

matchNested(): Match inside nested elements