TEMPO (Transcriptomic Expression Mapping & Pipeline Observatory)

In this project, you will develop TEMPO: an interactive platform for preprocessing and analysing gene expression data. The aim is to produce a user-friendly and flexible R-based pipeline, enabling researchers to run robust and reproducible data analysis across diverse datasets.

The project will extend the existing TEMPO GitHub repository by integrating workflow management tools, templated reporting, and clear documentation so that the pipeline can be easily adopted and executed by others.

A minimally viable version will:

1. Finalise the existing TEMPO R package to support basic analysis of gene expression data. 2. Implement a Snakemake workflow to execute the analysis pipeline in a reproducible manner. 3. Produce an interactive Quarto or R Markdown report that summarises results.

A fully completed version would include: 1. A polished TEMPO R package that can be installed from GitHub and contains modular functions for quality control, exploratory analysis, and data visualisation. 2. Comprehensive package documentation and a public walkthrough using open datasets (e.g., GEO), hosted via GitHub Pages. 3. A flexible interactive HTML report (Quarto/Rmd), allowing users to explore data and results. 4. A workflow-managed execution layer (Snakemake/targets) supporting batch processing and reproducibility across platforms. 5. A Docker/Singularity container to ensure fully portable execution of the pipeline on any machine, including options for local (secure) computation.