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04.12.2022 16:58:34
mar622 - Profile Module R programming for (meta)-genomic sequence analysis (Complete module description)
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Module label Profile Module R programming for (meta)-genomic sequence analysis
Modulkürzel mar622
Credit points 6.0 KP
Workload 180 h
(
Präsenzzeit: 54 Stunden, Selbststudium: 126 Stunden
)
Institute directory Institute for Chemistry and Biology of the Marine Environment
Verwendbarkeit des Moduls
  • Master's Programme Marine Environmental Sciences (Master) > Mastermodule
  • Master's Programme Microbiology (Master) > Mastermodule
Zuständige Personen
Prerequisites
Participation in the course „Introduction in sequencing and sequence analysis”. Previous programming experience is not required.
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 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

Module contents

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
Language of instruction English
Duration (semesters) 1 Semester
Module frequency is currently not offered
Module capacity 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
Form of instruction Comment SWS Frequency Workload of compulsory attendance
Seminar 2 SoSe 28
Practical training 2 SoSe 28
Präsenzzeit Modul insgesamt 56 h
Examination Prüfungszeiten Type of examination
Final exam of module
Announced during the course.
Written protocol (80%) and class participation (20%).