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Linux (and another software)

By vojta , 9 September 2024

Course of work with molecular data in R 2025

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.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 9 September 2024

Course of work in Linux command line not only for MetaCentrum 2025

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Články
Linux (and another software)
openSUSE
Faculty of Science, Charles University
Teaching
By vojta , 13 May 2024

Target enrichment in taxonomy, HybSeq course 2024

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Články
Bioinformatics
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Science, research, biology
Teaching
By vojta , 27 September 2023

Course of work with molecular data in R 2024

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.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 27 September 2023

Course of work in Linux command line not only for MetaCentrum 2024

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Články
Linux (and another software)
openSUSE
Faculty of Science, Charles University
Teaching
By vojta , 29 May 2023

Target enrichment in taxonomy, HybSeq course 2023

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Články
Bioinformatics
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Science, research, biology
Teaching
By vojta , 12 October 2022

Course of work with molecular data in R 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.

Články
Phylogeny
Phylogeography
Linux (and another software)
Population genetics
Faculty of Science, Charles University
R
Taxonomy
Teaching
By vojta , 12 October 2022

Course of work in Linux command line not only for MetaCentrum 2023

Don’t be afraid of command line! It is friendly and powerful tool allowing to process large data and automate tasks. Practically identical is command line also in Apple macOS, BSD and another UNIX-based systems, not only in Linux. The course is designed for total beginners as well as intermediate advanced students. The only requirement is an interest (or need) to work in command line, typically on Linux computing server.

Články
Linux (and another software)
openSUSE
Faculty of Science, Charles University
Teaching
By vojta , 3 June 2022

Target enrichment for plant systematics - HybSeq course 2022

Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest papers from the field, probe design, laboratory and computer part. Several methodological approaches to data analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS library preparation (using sonicator) and enrichment.

Články
Bioinformatics
Phylogeny
HybSeq
Linux (and another software)
Faculty of Science, Charles University
Science, research, biology
Teaching
By vojta , 11 January 2022

Virtual machine for my courses

For my courses ofwork in Linux command line not only for MetaCentrum and with molecular data in R I provide VirtualBox image, which allows to run complete desktop Linux (in this case openSUSE Leap) with all preinstalled applications needed for both courses. It's easy way how to get fully working Linux to play with. It requires at least bit powerful notebook, e.g. at least quad-core with at least 8 GB RAM, but more is better.

Články
Bioinformatics
Linux (and another software)
openSUSE
Faculty of Science, Charles University
Teaching

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