Stud.IP Uni Oldenburg
Universität Oldenburg
28.02.2021 14:44:27
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
Modulcode mar622
Kreditpunkte 6.0 KP
Workload 180 h
(

Präsenzzeit: 54 Stunden, Selbststudium: 126 Stunden

)
Fachbereich/Institut Institut für Chemie und Biologie des Meeres (ICBM)
Verwendet in Studiengängen
  • Master Microbiology (Master) > Mastermodule
Ansprechpartner/-in
Modulverantwortung
Prüfungsberechtigt
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

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 below. 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.

 

The course will cover the following topics:

·        programming in R using an integrated development environment (RStudio)

·        working with strings (stringr package)

·        working with lists and data frames (readr and dplyr package)

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

·        (meta)-genomic and data visualization (ggplot2, Gviz)

·        Creating sequence / metadata databases

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

·        reporting in R (Rmarkdown and Knitr packages)

·        managing code (Roxygen2 package)

microbial genome annotation using R.
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 Seminar (2 SWS), Practical (2 SWS)
Vorkenntnisse / Previous knowledge Participation in the course „Introduction in sequencing and sequence analysis”. Previous programming experience is not required.
Lehrveranstaltungsform Kommentar SWS Angebotsrhythmus Workload Präsenzzeit
Seminar 2.00 SoSe 28 h
Praktikum 2.00 SoSe 28 h
Präsenzzeit Modul insgesamt 56 h
Prüfung Prüfungszeiten Prüfungsform
Gesamtmodul
Will be announced during the course
Written protocol (80%) and class participation (20%)