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Introduction to AnnotationGx

Jermiah Joseph

BHKLab
Introduction.Rmd

Basics

Install AnnotationGx

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. AnnotationGx is a R package

TODO::after submitting to cran update this

Citing AnnotationGx

We hope that AnnotationGx will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

## Citation info
citation("AnnotationGx")
#> To cite package 'AnnotationGx' in publications use:
#> 
#>   Joseph J, Eeles C, Haibe-Kains B (2025). _AnnotationGx: AnnotationGx:
#>   A package for building, updating and querying an annotation database
#>   for pharmaco-genomic data_. R package version 0.0.0.9097,
#>   <https://bhklab.github.io/AnnotationGx/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {AnnotationGx: AnnotationGx: A package for building, updating and querying an
#> annotation database for pharmaco-genomic data},
#>     author = {Jermiah Joseph and Christopher Eeles and Benjamin Haibe-Kains},
#>     year = {2025},
#>     note = {R package version 0.0.0.9097},
#>     url = {https://bhklab.github.io/AnnotationGx/},
#>   }

Quick start to using AnnotationGx 

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.3 (2025-02-28)
#>  os       Ubuntu 24.04.2 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en
#>  collate  C.UTF-8
#>  ctype    C.UTF-8
#>  tz       UTC
#>  date     2025-03-27
#>  pandoc   3.1.11 @ /opt/hostedtoolcache/pandoc/3.1.11/x64/ (via rmarkdown)
#>  quarto   NA
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package      * version    date (UTC) lib source
#>  AnnotationGx * 0.0.0.9097 2025-03-27 [1] local
#>  backports      1.5.0      2024-05-23 [1] RSPM
#>  bslib          0.9.0      2025-01-30 [1] RSPM
#>  cachem         1.1.0      2024-05-16 [1] RSPM
#>  checkmate      2.3.2      2024-07-29 [1] RSPM
#>  cli            3.6.4      2025-02-13 [1] RSPM
#>  data.table     1.17.0     2025-02-22 [1] RSPM
#>  desc           1.4.3      2023-12-10 [1] RSPM
#>  digest         0.6.37     2024-08-19 [1] RSPM
#>  evaluate       1.0.3      2025-01-10 [1] RSPM
#>  fastmap        1.2.0      2024-05-15 [1] RSPM
#>  fs             1.6.5      2024-10-30 [1] RSPM
#>  htmltools      0.5.8.1    2024-04-04 [1] RSPM
#>  jquerylib      0.1.4      2021-04-26 [1] RSPM
#>  jsonlite       1.9.1      2025-03-03 [1] RSPM
#>  knitr          1.50       2025-03-16 [1] RSPM
#>  lifecycle      1.0.4      2023-11-07 [1] RSPM
#>  pkgdown        2.1.1      2024-09-17 [1] any (@2.1.1)
#>  R6             2.6.1      2025-02-15 [1] RSPM
#>  ragg           1.3.3      2024-09-11 [1] RSPM
#>  rlang          1.1.5      2025-01-17 [1] RSPM
#>  rmarkdown      2.29       2024-11-04 [1] RSPM
#>  sass           0.4.9      2024-03-15 [1] RSPM
#>  sessioninfo  * 1.2.3      2025-02-05 [1] RSPM
#>  systemfonts    1.2.1      2025-01-20 [1] RSPM
#>  textshaping    1.0.0      2025-01-20 [1] RSPM
#>  xfun           0.51       2025-02-19 [1] RSPM
#>  yaml           2.3.10     2024-07-26 [1] RSPM
#> 
#>  [1] /home/runner/work/_temp/Library
#>  [2] /opt/R/4.4.3/lib/R/site-library
#>  [3] /opt/R/4.4.3/lib/R/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────