Package: pogos 1.27.1

VJ Carey

pogos: PharmacOGenomics Ontology Support

Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.

Authors:Vince Carey <[email protected]>

# Install 'pogos' in R:

install.packages('pogos', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CCLE_drts - Compounds_v1: serialization of compounds info from PharmacoDb v1
cell_lines_v1 - Compounds_v1: serialization of compounds info from PharmacoDb v1
compounds_v1 - Compounds_v1: serialization of compounds info from PharmacoDb v1
datasets_v1 - Compounds_v1: serialization of compounds info from PharmacoDb v1
tissues_v1 - Compounds_v1: serialization of compounds info from PharmacoDb v1

On BioConductor:pogos-1.27.1(bioc 3.21)pogos-1.26.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated 2 months agofrom:c609080a26. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

Vincent J. Carey, stvjc at channing.harvard.edu

Last update: 2025-01-15
Started: 2017-09-30

Help page	Topics
subscripting on DRProfSet extracts a profile for a single drug whose name constitutes the index	[,DRProfSet,character,ANY,ANY-method
convert binary output of GET()$content to list	basicDecoder
compounds_v1: serialization of compounds info from PharmacoDb v1	CCLE_drts cell_lines_v1 compounds_v1 datasets_v1 tissues_v1
initial version of compound browser over pharmacoDb cells	compoundsByCell
DRProfSet is a class for managing dose-response information about cell lines from a pharmacogenomics dataset	DRProfile-class DRProfSet DRProfSet-class getDrugs getDrugs,DRProfSet-method plot,DRProfSet,missing-method
DRTraceSet class manages dose-response information for a single cell line, multiple drugs	DRTraceSet DRTraceSet-class plot,DRTraceSet,missing-method
obtain an example trace set stored locally, for irinotecan and selected cell lines	iriCCLE
very simple query formulation, build queries using endpoints of bhklab PharmacoDB API	rxdbQuery_v1
enumerate top level endpoint terms for bhklab PharmacoDB API	topEndpoints_v1
trace extractor	traces