mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Complete module description)

Präsenzzeit: 54 Stunden, Selbststudium: 126 Stunden

DNA sequencing has become a routine method in microbiology research. Most of the times, sequence analysis requires knowledge of a programming language.  One of the programming languages most used for this purpose is R.

After successful participation the students will have the competence to understand, interpret and carry out simple genome sequence analyses. They will acquire transferable skills in using R

The course will cover the following topics:

1.     programming in R using an integrated development environment (RStudio)

2.     working with strings (stringr package)

3.     working with lists and data frames (readr and dplyr package)

4.     sequence analysis (seqinr, Bioconductor packages: Biostrings, GenomicRanges, Decipher)

5.     (meta)-genomic and data visualization  (ggplot2, Gviz)

6.     Creating sequence / metadata dabases

7.     Accessing and mining sequence / metadata databases though R based web applications (Shiny, DT and Shinyjs packages)

8.     reporting in R (Rmarkdown and Knitr packages)

9.     managing code (Roxygen2 package)

10.  microbial genome annotation using R.
 

A single, introductory lecture will be offered within the first day of the course. Then, the course will be structured in programming exercises which cover all topics listed. The exercises are designed to exemplify the use R programming within the framework of microbial (meta)-genome analysis.

In addition to the teacher–student sessions, the students will work on individual projects. Each student will receive a short microbial genome (e.g. viral genome), and will analyze it by building custom, self-programmed pipelines. The output from the individual projects will consist in an analysis report prepared in Rmarkdown and Knitr packages. The report will include both the R code and the genome analysis results.