Stud.IP Uni Oldenburg
Universität Oldenburg
03.12.2021 13:34:44
mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Vollständige Modulbeschreibung)
Originalfassung Englisch PDF Download
Modulbezeichnung Profile Module R programming for (meta)-genomic sequence analysis
Modulkürzel mar622
Kreditpunkte 6.0 KP
Workload 180 h
(

Präsenzzeit: 54 Stunden, Selbststudium: 126 Stunden

)
Einrichtungsverzeichnis Institut für Chemie und Biologie des Meeres (ICBM)
Verwendbarkeit des Moduls
  • Master Marine Umweltwissenschaften (Master) > Mastermodule
  • Master Microbiology (Master) > Mastermodule
Zuständige Personen
Moraru, Liliana Cristina (Modulverantwortung)
Teilnahmevoraussetzungen
Participation in the course „Introduction in sequencing and sequence analysis”. Previous programming experience is not required.
Kompetenzziele

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

Modulinhalte

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.

Literaturempfehlungen
will be announced
Links
Unterrichtssprache Englisch
Dauer in Semestern 1 Semester
Angebotsrhythmus Modul jährlich
Aufnahmekapazität Modul 15 (
Proportionale Aufteilung zwischen Master MUWI und Master Microbiology
)
Modullevel / module level AC (Aufbaucurriculum / Composition)
Modulart / typ of module Wahlpflicht / Elective
Lehr-/Lernform / Teaching/Learning method Blockveranstaltung:
SE/PR: R programming for (meta)-genomic sequence analysis (4 SWS, 6 KP)
Vorkenntnisse / Previous knowledge Teilnahme an mar454 Einführung in die DNA-Sequenzierung und Sequenzanalyse. Grundlagen der Programmierung in R, Grundlagen der Molekularen Taxonomie
Lehrveranstaltungsform Kommentar SWS Angebotsrhythmus Workload Präsenz
Seminar
2 SoSe 28
Praktikum
2 SoSe 28
Präsenzzeit Modul insgesamt 56 h
Prüfung Prüfungszeiten Prüfungsform
Gesamtmodul
Will be announced during the course
Written protocol (80%) and class participation (20%)