Bioinformatics data visualization in R, produced during the HackBio Data Visualization in Bio (vizbio) internship.
The internship runs from a first R script and a technical writing piece, through exploratory visualization of independent datasets, to the reproduction of a published seven-panel figure and an interactive Shiny web application.
| Stage | Project | What it covers |
|---|---|---|
| 0 | Technical Writing and First Steps in R | An article on visualization for healthcare translation. First R script using lists and string handling. |
| 1 | Functions, Loops and Input Validation | A GC content calculator and a protein molecular weight calculator: both are reusable functions with input validation. |
| 2 | Data Visualization in R | Exploratory visualization of independent datasets. Reproduction of a seven-panel figure from a 2025 Nature Communications paper. |
| 3 | Cell Type Snapshot Explorer | An interactive Shiny web application for exploring marker genes, deployed on shinyapps.io. |
Each stage folder has its own README covering the task, the data, the code and the reasoning behind each design decision.
Across the two visualization stages: boxplots, scatter and volcano plots, quadrant plots, clustered and annotated heatmaps, pathway enrichment heatmaps, correlation matrices, bubble plots, stacked bar charts, kernel density plots, directed network graphs, multi-panel figure assembly.
ggplot2 · ComplexHeatmap · pheatmap · igraph · shiny · DT · dplyr · tidyr · readxl · patchwork · cowplot
- Gene expression and differential expression results (HBR vs UHR) — provided by HackBio · Stage 2
- Breast Cancer Wisconsin (Diagnostic) Dataset · Stage 2
- RNA kinetics during Salmonella infection — Xiong, Z., Wu, R., Wang, Y. et al. scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection. Nat Commun 16, 7937 (2025). https://doi.org/10.1038/s41467-025-63155-1 · Stage 2
- Simulated single-cell RNA-seq dataset (expression matrix, cell metadata, UMAP coordinates) — provided by HackBio · Stage 3
All work was completed as part of the HackBio Data Visualization in Bio (vizbio) bioinformatics internship.