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Add Course Title Informatics Guide

Software used during the course

Software used during the course

Software Version (if not latest) Module Notes
Chrome Latest All modules Required for browser-based tools
Firefox Latest All modules Alternative browser support
Miniforge 25.3.1 General setup Used for managing Python/R environments
Python 3.12.11 General setup Core environment for notebooks
Jupyter Notebook 7.4.7 MPRA QC Used for interactive analysis
JupyterLab 4.4.9 MPRA QC Enhanced notebook interface
marimo 0.16.5 MPRA QC Lightweight notebook runner
R 4.3.3 MPRA QC Used for data analysis and visualisation
RStudio 2025.09.2+418 MPRA QC IDE for R
Enrich2 2.0.2 MAVE Data Analysis II For variant enrichment analysis
CountESS 0.1.10 MAVE Data Analysis II For sequence counting
tidyverse Latest MPRA QC R package suite for data wrangling
ggplot2 Latest MPRA QC R package for plotting
dplyr Latest MPRA QC R package for data manipulation
Microsoft Excel Latest Clinical validation For reviewing clinical datasets
Docker Latest MAVE Data Analysis I Used for containerised environments
Nextflow Latest MAVE Data Analysis I Workflow management system
QUANTS 3.1.0.0 MAVE Data Analysis I Analysis software for MAVE
MAVE-QC v0.2.9.229 MAVE Data Analysis I QC pipeline for MAVE data
Ensembl VEP 115.2 Annotation 23 GB cache required for local use

Bookmarks and Resources

Resource Link
DECIPHER https://www.deciphergenomics.org/
Mol* Viewer https://molstar.org/viewer/
ClinVar https://www.ncbi.nlm.nih.gov/clinvar/

Rolling Nextflow to version 23.10.1

notebook bash kernel

pip install bash_kernel
python -m bash_kernel.install

netflow roll back

export NXF_VER=23.10.1
curl -s https://get.nextflow.io | bash
mv nextflow ~/.local/bin/nextflow
chmod +x ~/.local/bin/nextflow

Informatics Set-Up

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.)
  • Docker Installation Guide – Step-by-step guide for installing Docker on Windows, macOS, and Linux.

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

Citing and Re-using Course Material

The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Creative Commons Licence

Each course landing page is assigned a DOI via Zenodo, providing a stable and citable reference. These DOIs can be found on the respective course landing pages and can be included in CVs or research publications, offering a professional record of the course contributions.

Interested in attending a course?

Take a look at what courses are coming up at Wellcome Connecting Science Courses & Conference Website.

Wellcome Connecting Science GitHub Home Page

For more information or queries, feel free to contact us via the Wellcome Connecting Science website.
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