Syllabus
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).
Annotation
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.