Bioinformatics: R Shiny Educational App - Transcriptomics Pipeline

Level 2: Develop an educational app that applies the main workflow used in large-scale data analysis.

Paper used in pipeline: Identification of and enriched pathways in lung cancer using bioinformatics analysis

Data: GSE19804

Technical Objectives

  • Generalize the transcriptomics workflow introduced in the Level 1 Project
  • Understand the methods of analysis and their applications
  • Use Rshiny to develop an educational website

Soft Skills Objectives

  • Reading and understanding scientific papers
  • Project management
  • Virtual collaboration and teamwork
  • Technical presentation
  • Time management and much more
  • Leadership & mentoring (student leads)

Level 1: Introduce students to bioinformatics and the main workflow used in large-scale data analysis.

Paper used in pipeline: Identification of and enriched pathways in lung cancer using bioinformatics analysis

Data: GSE19804

Technical Objectives

  • Introduction to bioinformatics and the different types of -omics data
  • Application of the basic pipeline used in large-scale data analysis: data collection, QC, statistical analysis, and functional interpretation of results
  • Learning how to work through a coherent workflow and interpret output results and relate them to biological problems
  • Learning the basics of RStudio and R programming
  • Introduction to Bioconductor and packages used in transcriptomics data analysis relevant to the above-mentioned pipeline
  • Learning how to troubleshoot in R and read R documentation
  • Using free, public bioinformatics tools used for functional analysis of transcriptomics results

Soft Skills Objectives

  • Reading and understanding scientific papers
  • Project management
  • Virtual collaboration and teamwork
  • Technical presentation
  • Time management and much more
  • Leadership & mentoring (student leads)

NOTE: Kick-off meetings follow the modules of the Level 1 project. Separate meetings are held for the R Shiny App Development.