g708 / ki-course-5633

Assignments for " Bioinformatics Analysis and Visualisation of Medical Genomics Data", March 2023

KI-course-5633

Assignments for " Bioinformatics Analysis and Visualisation of Medical Genomics Data", March 2023

Environment

Environment for RStudio is managed by Docker.

• R version 4.2.2 (2022-10-31)

• Platform: x86_64-pc-linux-gnu (64-bit)

• Running under: Ubuntu 22.04.1 LTS

• tidyverse_2.0.0

• BiocManager_1.30.19

• ggplot2_3.4.1

Run

All required environment is contain in Docker image.

In vscode

Requierment: Dev Containers extention

Use Dev Containers extention to open folder in container. Access http://localhost:8787/ on browser and open Rstudio.

In command line

After run docker image, access http://localhost:8787/ on browser and open Rstudio.

To share the assignments and notebooks.

All tastk for week1 is in Week1 folder. Task 2 and 3 is setting environment so there is no document.

I use R notebook to write my documents for task 4 to 8 and save as github_document. By this format, R notebook is able to rendering the .Rmd document on Github.

• Task1
• Task4
• Task5
• Task6
• Task7
• Task8

.Rmd and .nb.html format is not able see on github repository and both .Rmd and .nb.html must be download and open on Rstudio to see visualization.