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An R package to query various bio/chem-informatics databases APIs to construct annotation files.

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GPL-3.0
LICENSE.md
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bhklab/AnnotationGx

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AnnotationGx

GitHub R package version GitHub R package version (development) CRAN/METACRAN Version

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Installation

You can install from github using:

remotes::install_github(
    "bhklab/AnnotationGx", 
    build_manual=TRUE, 
    build_vignettes=TRUE
)

Example

First load the package:

library(AnnotationGx)
help(package="AnnotationGx")

Annotate cell line using cellosaurus:

name <- "A549"

mapCell2Accession(name)

Annotate drugs using PubChem:

drugs <- c(
  "Aspirin", "Erlotinib", "Acadesine", 
  "Camptothecin", "Vincaleukoblastine", "Cisplatin"
)

(compound_2_cids <- mapCompound2CID(drugs, first = TRUE))
mapCID2Properties(
    ids = compound_2_cids$cids,
    properties = c("Title", "MolecularFormula", "InChIKey", "MolecularWeight")
)

annotatePubchemCompound(
    cids = compound_2_cids$cids,, 
    heading = "CAS"
)

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An R package to query various bio/chem-informatics databases APIs to construct annotation files.

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License

MIT, GPL-3.0 licenses found

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MIT
LICENSE
GPL-3.0
LICENSE.md

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