Contents

1 DockerHub

orthogene is now available via DockerHub as a containerised environment with Rstudio and all necessary dependencies pre-installed.

1.1 Installation

1.2 Method 1: via Docker

First, install Docker if you have not already.

Create an image of the Docker container in command line:

docker pull neurogenomicslab/orthogene

Once the image has been created, you can launch it with:

docker run \
  -d \
  -e ROOT=true \
  -e PASSWORD="<your_password>" \
  -v ~/Desktop:/Desktop \
  -v /Volumes:/Volumes \
  -p 8787:8787 \
  neurogenomicslab/orthogene

1.2.1 NOTES

  • Make sure to replace <your_password> above with whatever you want your password to be.
  • Change the paths supplied to the -v flags for your particular use case.
  • The -d ensures the container will run in “detached” mode, which means it will persist even after you’ve closed your command line session.
  • The username will be “rstudio” by default.
  • Optionally, you can also install the Docker Desktop to easily manage your containers.

1.3 Method 2: via Singularity

If you are using a system that does not allow Docker (as is the case for many institutional computing clusters), you can instead install Docker images via Singularity.

singularity pull docker://neurogenomicslab/orthogene

1.4 Usage

Finally, launch the containerised Rstudio by entering the following URL in any web browser: http://localhost:8787/

Login using the credentials set during the Installation steps.

2 Session Info

utils::sessionInfo()
## R version 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] orthogene_1.14.0 BiocStyle_2.36.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6              babelgene_22.9           
##  [3] xfun_0.52                 bslib_0.9.0              
##  [5] ggplot2_3.5.2             htmlwidgets_1.6.4        
##  [7] rstatix_0.7.2             lattice_0.22-7           
##  [9] vctrs_0.6.5               tools_4.5.0              
## [11] generics_0.1.3            yulab.utils_0.2.0        
## [13] parallel_4.5.0            tibble_3.2.1             
## [15] pkgconfig_2.0.3           Matrix_1.7-3             
## [17] data.table_1.17.0         homologene_1.4.68.19.3.27
## [19] ggplotify_0.1.2           lifecycle_1.0.4          
## [21] compiler_4.5.0            farver_2.1.2             
## [23] treeio_1.32.0             munsell_0.5.1            
## [25] carData_3.0-5             ggtree_3.16.0            
## [27] ggfun_0.1.8               gprofiler2_0.2.3         
## [29] htmltools_0.5.8.1         sass_0.4.10              
## [31] yaml_2.3.10               lazyeval_0.2.2           
## [33] Formula_1.2-5             plotly_4.10.4            
## [35] pillar_1.10.2             car_3.1-3                
## [37] ggpubr_0.6.0              jquerylib_0.1.4          
## [39] tidyr_1.3.1               cachem_1.1.0             
## [41] grr_0.9.5                 abind_1.4-8              
## [43] nlme_3.1-168              tidyselect_1.2.1         
## [45] aplot_0.2.5               digest_0.6.37            
## [47] dplyr_1.1.4               purrr_1.0.4              
## [49] bookdown_0.43             fastmap_1.2.0            
## [51] grid_4.5.0                colorspace_2.1-1         
## [53] cli_3.6.4                 magrittr_2.0.3           
## [55] patchwork_1.3.0           broom_1.0.8              
## [57] ape_5.8-1                 scales_1.3.0             
## [59] backports_1.5.0           httr_1.4.7               
## [61] rmarkdown_2.29            ggsignif_0.6.4           
## [63] evaluate_1.0.3            knitr_1.50               
## [65] viridisLite_0.4.2         gridGraphics_0.5-1       
## [67] rlang_1.1.6               Rcpp_1.0.14              
## [69] glue_1.8.0                tidytree_0.4.6           
## [71] BiocManager_1.30.25       jsonlite_2.0.0           
## [73] R6_2.6.1                  fs_1.6.6