wtchoga/bioinformatics-series-botswana

Bioinformatics, AI and Data Science Training - Botswana (BHP/HSPH). Forked and customised from elsherbini/durban-data-science-for-biology. # Bioinformatics Series in Botswana Workshop website for **Bioinformatics, AI and Data Science Training**, hosted in Gaborone by the Botswana Harvard Partnership (BHP) and the Harvard T.H. Chan School of Public Health (HSPH). ## Instructions on contributing to the website 1. clone the repo locally 2. make changes - you can preview changes locally by clicking "Render Website" in the Build tab in RStudio, or by running `quarto preview` in the terminal. 3. commit changes and push to the `bhl-customisation` branch 4. run `quarto publish gh-pages` to render the website and update the github.io content ### Requirements - Quarto 1.4 or later - R 4.3.1 or later ```r install.packages(c("tidyverse", "here", "knitr", "rmarkdown", "quarto")) ``` Session materials need more — see installation-instructions.qmd for the full list, including the Bioconductor packages (`DESeq2`, `edgeR`, `limma`, `mixOmics`, `ggtree`) and the standalone tools (AliView, IQ-TREE 3, FigTree 1.4.4, BEAST 1.10.5). ## Repository layout ``` ├── _quarto.yml site config, navbar and sidebar ├── index.qmd landing page: overview, schedule, instructors ├── about.qmd teaching team, partners, contact ├── past_workshops.qmd Sept 2025 Virus Evolution & Genomics Workshop ├── installation-instructions.qmd ├── exercises.qmd Day 1 + Day 2 exercises └── materials/ ├── 1-welcome/ welcome session ├── 2-ml-session/ Random Forest — HIV/SIV rebound ├── 3-bulk-rnaseq/ DESeq2 + GSEA ├── 1-intro-bioinfo-ai/ what is bioinformatics / AI / data science ├── 2-ai-application/ ML foundations → LLMs (5 modules) ├── 3-bioinformatics-application/ QC → phylogenetics (4 modules) ├── 4-hands-on/ mtDNA case study (synthetic data) ├── 5-survey/ feedback ├── 6-mutations/ HIV-1 mutations & minority variants └ …