Software used during the course
| Software | Version | Module(s) | Notes |
|---|---|---|---|
| PRSice-2 | v2.3.5 | Advanced Analyses (Wednesday) | Used for PRS calculation and analysis |
| PRS-CSx | v1.1.0 | Practical Session – PRS-CSx (Thursday) | Polygenic scoring across ancestries |
| BridgePRS | v1.0.3 | Practical Session – BridgePRS (Wednesday) | Software benchmarking and ancestry-aware PRS |
| R | v4.2.3 | Bash & R Intro (Monday), PRS-related modules | Required for all R-based analysis |
| PLINK | v1.9 (beta 7) | Introduction to PLINK I & II (Monday) | Used for QC and GWAS |
| Samtools | v1.19.2 | Data preprocessing sessions | Handling BAM files |
| BCFtools | v1.19 | Variant processing | Working with VCFs |
| RStudio | Latest | All R-based sessions | GUI for R |
| Rcpp | Latest | R sessions | Required dependency |
| RFMix2 | Latest | ||
| reshape2 | Latest | R sessions | Data reshaping |
| viridisLite | Latest | R sessions | Plotting color palettes |
| viridis | Latest | R sessions | Color palettes for ggplot2 |
| BiocManager | Latest (Bioconductor v3.18) | R sessions | Used to install Bioconductor packages |
| GenomicRanges | Latest | R sessions | Installed via BiocManager |
| dplyr | Latest | R sessions | Data manipulation |
| tidyr | Latest | R sessions | Data tidying |
| vcfR | Latest | R sessions | VCF file manipulation in R |
| memuse | Latest | R sessions | Memory usage diagnostics |
| data.table | Latest | R sessions | Efficient data handling |
| panelr | Latest | R sessions | Panel data analysis |
ℹ️ Please ensure all software and R packages are installed prior to their respective sessions to allow smooth participation in practical exercises.
For installation and setup, please refer to the following guides:
- Oracle VM VirtualBox Installation Guide – Detailed instructions for installing and configuring VirtualBox on different operating systems. (Note: Separate installations are needed for Intel-based and ARM-based Macs, and the VDI files will differ.)
The Host Operating System Requirements are:
- RAM requirement: 8GB (preferably 12GB)
- Processor requirement: 4 processors (preferably 8)
- Hard disk space: 200GB
- Admin rights to the computer
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