SubjectsSubjects(version: 873)
Course, academic year 2020/2021
  
Course of work with molecular data in R - MB120C16
Title: Kurz práce s molekulárními daty v R
Czech title: Kurz práce s molekulárními daty v R
Guaranteed by: Department of Botany (31-120)
Faculty: Faculty of Science
Actual: from 2019
Semester: winter
E-Credits: 2
Examination process: winter s.:
Hours per week, examination: winter s.:0/4 C [days/semester]
Capacity: 35
Min. number of students: unlimited
State of the course: taught
Language: Czech
Additional information: https://trapa.cz/cs/kurz-molekularni-data-r-2020
Guarantor: Mgr. Vojtěch Zeisek, Ph.D.
Teacher(s): Mgr. Vojtěch Zeisek, Ph.D.
Opinion survey results   Examination dates   Schedule   
Annotation -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (07.10.2019)
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.
The course contains theory of used methods, tutorials with test data, tasks for individual work of participants, and more.
Previous knowledge of R is useful, but not necessary. At least basic knowledge of molecular biology is required, previous knowledge about any methods how to analyse DNA data is recommended.
The course will be taught 5 days, while 4 days are for teaching and last day is for exams and individual consultations. Course participants can stay this last day (which is recommended), but it is not conditional.
If there is at least one participant not speaking Czech, the course will be in English.
The course will be taught January 27-31 2020, Benátská 2, lecture room B12, from 9:00 to 16-17:00 (with enough breaks).
Literature -
Requirements to the exam -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (04.10.2017)
  • Active participation.
  • Asking and answering on-topic questions during the course.
  • Loading of any molecular data into R (own, exemplary data from some R package, or from on-line database) and doing several appropriate analysis (according to data type), it is possible to use Internet, documentation, etc.
  • Write to Wikipedia at least one page about any topic related to the course. It can be translation, edition of an existing page, it can be splitted into several articles, etc. Student should use native Wikipedia according to her/his language (so preferebly not English).
Syllabus -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (23.09.2019)

List of topics (might be edited according to wishes of participants, speed, etc.):

  • Basic work in R - how to enter commands, install packages, read help, types of variables, indexes, etc.
  • Bioconductor
  • Load and export molecular data of various types and formats.
  • Download molecular data from on-line databases
  • Extractions of SNP from sequencing data
  • Extraction of polymorphism from sequences
  • Mikrosatellites, AFLP, SNP, sequences, ...
  • Manipulations with data, conversions among formats
  • Distance matrices, import of custom matrices
  • Export of data
  • Basic statistics
  • PCoA
  • Phylogenetic trees (NJ, UPGMA, ML) and display and test
  • MSN
  • Basic statistics, genetic indices heterozygosity, HWE, F-statistics
  • DAPC
  • Whole genome SNP data
  • Spatial analysis - Mantel test, Moran’s I, Monmonier, sPCA, ...
  • Basic map creation
  • Structure
  • Alignments
  • Manipulations with trees, work with big sets of trees
  • Phylogenetic independent contrast
  • Phylogenetic autocorrelation
  • Phylogenetic PCA
  • Ancestral state reconstruction
  • Additional extending topics

There will be space available during the last day for another special questions of participants, exams and consultation of participants' own data (facultative).

Entry requirements -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (23.09.2019)

Don't be afraid of R. :-)

Previous knowledge of R is useful, but not necessary. At least basic knowledge of molecular biology is required, previous knowledge about any methods how to analyse DNA data is recommended. I recommend to follow courses R for life - MB120P147E a Use of molecular markers in plant systematics and population biology - MB120P44 (optionally also with practical lessons I and II), and Plant population genetics - MB120P145, or anything similar, prior to this course.

For course you need

  • Own computer to work.
  • Working Wi-Fi. Eduroam (set it up using faculty or recommended general instructions) or in application form You can ask for temporary password.
  • Installed R. I also recommend to install some graphical user interface like RStudio, RKWard, R commander or some similar according to your choice.
  • If you have experience with R, you can save some work by installing required R packages in advance. I'll send instruction prior to the course.
Registration requirements -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (11.10.2016)

I'd be glad if participants could fill a short questionary which will help me with preparation of the course and communication.

 
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