| Software | URL for software / Software version |
| R/CRAN | https://cran.ma.imperial.ac.uk/ |
| RStudio | https://download1.rstudio.org/electron/jammy/amd64/rstudio-2023.12.1-402-amd64.deb |
| Java 11 or later (We recommend that you install Java through SDKMAN!, and that you use the latest LTS version of Corretto or Temurin.) | sdkman! https://sdkman.io/sdk then install java 17.0.6-amzn |
| Nextflow | curl -s https://get.nextflow.io | bash |
| dplyr | https://dplyr.tidyverse.org/ |
| tibble | https://tibble.tidyverse.org/ |
| ggthemes | https://exts.ggplot2.tidyverse.org/ggthemes.html |
| scales | https://scales.r-lib.org/ |
| ggplot2 | https://ggplot2.tidyverse.org/ |
| patchwork | https://cran.r-project.org/web/packages/patchwork/index.html |
| DESeq2 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| pcaExplorer | https://www.bioconductor.org/packages/release/bioc/html/pcaExplorer.html |
| tidyverse (R package) |
https://www.tidyverse.org/packages/ |
| synapser (R package) | https://github.com/Sage-Bionetworks/synapser |
| rmarkdown |
https://cran.r-project.org/web/packages/rmarkdown/index.html |
| knitr | https://cran.r-project.org/web/packages/knitr/index.html |
| plink 1.9 | https://www.cog-genomics.org/plink/ |
| PRS-CS | https://github.com/getian107/PRScs |
| Docker Engine | https://docs.docker.com/engine/install/ |
| Neo4j Desktop | https://neo4j.com/docs/desktop-manual/current/installation/ |
| Git | https://git-scm.com/ |
| libpng-dev | https://packages.ubuntu.com/jammy/libpng-dev |
| python3-pip | https://packages.ubuntu.com/jammy/python3-pip |
| python3-venv | https://packages.ubuntu.com/jammy/python3-venv |
| * before installing synapser R package run: python3 -m pip install virtualenv | This is required for reticulate, see https://github.com/rstudio/reticulate/issues/1509 |
| pandas | https://pandas.pydata.org/ |
| scanpy | https://scanpy.readthedocs.io/en/stable/ |
| seaborn | https://seaborn.pydata.org/ |
