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https://github.com/bhklab/annotationgx

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

https://github.com/bhklab/annotationgx

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 2
  • Watchers: 7
  • Forks: 1
  • Open Issues: 10
  • Releases: 1
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

AnnotationGx

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

R-CMD-check codecov Docker Pulls

Installation

You can install from github using:

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

Example

First load the package:

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

Annotate cell line using cellosaurus:

``` r name <- "A549"

mapCell2Accession(name) ```

Annotate drugs using PubChem:

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

(compound2cids <- mapCompound2CID(drugs, first = TRUE)) mapCID2Properties( ids = compound2cids$cids, properties = c("Title", "MolecularFormula", "InChIKey", "MolecularWeight") )

annotatePubchemCompound( cids = compound2cids$cids,, heading = "CAS" ) ```

Owner

  • Name: BHKLAB
  • Login: bhklab
  • Kind: organization
  • Location: Toronto, Ontario, Canada

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre

GitHub Events

Total
  • Issues event: 6
  • Member event: 1
  • Push event: 13
Last Year
  • Issues event: 6
  • Member event: 1
  • Push event: 13

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 11
  • Total pull requests: 42
  • Average time to close issues: 5 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.45
  • Average comments per pull request: 0.43
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 26
  • Average time to close issues: 1 day
  • Average time to close pull requests: about 3 hours
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.86
  • Average comments per pull request: 0.65
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sisiranair (6)
  • jjjermiah (5)
  • Urooj-M (1)
  • guanqiaofeng (1)
  • ChristopherEeles (1)
  • NiktaFeizi (1)
Pull Request Authors
  • jjjermiah (62)
  • ChristopherEeles (5)
  • ShahzadaShameelFarooq (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels
enhancement (1)

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • BiocParallel * imports
  • CoreGx * imports
  • R6 * imports
  • R6P * imports
  • checkmate * imports
  • crayon * imports
  • data.table * imports
  • httr * imports
  • jsonlite * imports
  • listenv * imports
  • memoise * imports
  • rlang * imports
  • rvest * imports
  • xml2 * imports
  • BiocStyle * suggests
  • DT * suggests
  • kableExtra * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v1 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite