Introduction to AnnotationGx

Jermiah Joseph

BHKLab

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 hosted on Bioconductor and can be installed using BiocManager.

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:
#> 
#>   Tran M, Joseph J, Eeles C, Haibe-Kains B (2026). _AnnotationGx:
#>   AnnotationGx: A package for building, updating and querying an
#>   annotation database for pharmaco-genomic data_. R package version
#>   0.99.1, <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 = {Michael Tran and Jermiah Joseph and Christopher Eeles and Benjamin Haibe-Kains},
#>     year = {2026},
#>     note = {R package version 0.99.1},
#>     url = {https://bhklab.github.io/AnnotationGx/},
#>   }

Quick start to using AnnotationGx

library("AnnotationGx")

sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] AnnotationGx_0.99.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] backports_1.5.0     digest_0.6.39       desc_1.4.3         
#>  [4] R6_2.6.1            fastmap_1.2.0       xfun_0.56          
#>  [7] cachem_1.1.0        knitr_1.51          htmltools_0.5.9    
#> [10] rmarkdown_2.30      lifecycle_1.0.5     cli_3.6.5          
#> [13] sass_0.4.10         pkgdown_2.2.0       data.table_1.18.2.1
#> [16] textshaping_1.0.4   jquerylib_0.1.4     systemfonts_1.3.1  
#> [19] compiler_4.5.2      tools_4.5.2         ragg_1.5.0         
#> [22] checkmate_2.3.4     evaluate_1.0.5      bslib_0.10.0       
#> [25] yaml_2.3.12         jsonlite_2.0.0      rlang_1.1.7        
#> [28] fs_1.6.6