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Course, academic year 2023/2024
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Course of work with molecular data in R - MB120C16
Title: Course of work with molecular data in R
Czech title: Kurz práce s molekulárními daty v R
Guaranteed by: Department of Botany (31-120)
Faculty: Faculty of Science
Actual: from 2023
Semester: winter
E-Credits: 2
Examination process: winter s.:
Hours per week, examination: winter s.:0/5, C [DS]
Capacity: 30
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Additional information: https://trapa.cz/cs/kurz-molekularni-data-r-2024
Note: enabled for web enrollment
Guarantor: Mgr. Vojtěch Zeisek, Ph.D.
Teacher(s): Mgr. Vojtěch Zeisek, Ph.D.
Annotation -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (03.10.2023)
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Their representative selection 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. The aim is to teach students how to analyze molecular data in R programming language, introduce available packages for their analysis and practical trying out to work with own or provided data.
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 analyze DNA data is recommended. The course is aiming primarily to Master and Ph.D. students, for Bachelor students only if they are highly advanced.
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.
The course will be taught from January 29 to February 2 2024, Benátská 2, lecture room B12, from 9:00 to 16-17:00 (with enough breaks). Depending on epidemiological situation the course can be in hybrid mode (not only in full attendance) or fully on-line only. Details will be updated according to the situation prior the course.
Consultations are possible any time after previous e-mail agreement.
Literature -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (11.11.2021)
Requirements to the exam -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (03.05.2021)
  • 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. (03.05.2021)

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
  • 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 (especially during the last day) for another special questions of participants, exams and consultation of participants' own data (optional).
Entry requirements -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (12.10.2022)

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 analyze 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. Course is primarily for Master and Ph.D. students, for Bachelor students only if they are very advanced.

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. If You do not wish to install everything, You can use prepared Linux image for VirtualBox containing everything needed.
Registration requirements -
Last update: Mgr. Vojtěch Zeisek, Ph.D. (03.05.2021)

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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