Stud.IP Uni Oldenburg
University of Oldenburg
18.01.2022 14:38:31
mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Course overview)
Institute for Chemistry and Biology of the Marine Environment 6 KP
Module components Semester courses Wintersemester 2021/2022 Examination
Seminar
Practical training
Notes for the module
Prerequisites
The course „Introduction in sequencing and sequence analysis”. Previous programming experience is not required.
Capacity / number of participants 15 (
Proportionale Aufteilung zwischen Master MUWI und Master Microbiology
)
Time of examination
Announced during the course.
Module examination
Written protocol (80%) and class participation (20%).
Skills to be acquired in this module
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 programing languages most used for this purpose is R. The course will cover the following topics:
I. programming in R using an integrated development environment (RStudio)
II. working with strings (stringr package)
III. working with lists and data frames (readr and dplyr package)
IV. sequence analysis (seqinr, Bioconductor packages: Biostrings, GenomicRanges, Decipher)
V. (meta)-genomic and data visualization (ggplot2, Gviz)
VI. Creating sequence / metadata dabases
VII. Accessing and mining sequence / metadata databases though R based web applications (Shiny, DT and Shinyjs packages)
VIII. reporting in R (Rmarkdown and Knitr packages)
IX. managing code (Roxygen2 package)
X. microbial genome annotation using R