Selle kursuse eesmärk on pakkuda põhiteadmisi Linuxi ja terminalikeskkonna kohta. Õpetame teile, kuidas juurde pääseda failidele ja kaustadele, liikuda nende vahel ja loodetavasti vabaneda hirmust kuskil tee peal kinni jääda. Eelnevaid teadmisi pole vaja.
Experiments designed to quantify gene expression often yield hundreds of genes that show statistically significant differences between groups of interest. Once differentially expressed genes are identified, enrichment analysis (EA) methods can be used to explore the biological functions associated with these genes. EA methods allow us to identify groups of genes (e.g. particular pathways) that are over-represented, thereby offering insights into biological mechanisms. One of the EA methods frequently used for high-throughput gene expression data analysis is Gene Set Enrichment Analysis (GSEA). This course will cover GSEA and alternative enrichment methods. Because the implementation of GSEA is directly linked to databases that annotate the function of genes in a cell, the course will also give an overview of functional annotation databases such as Gene Ontology.
Application deadline: 26 February 2024
The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. Next generation sequencing (NGS) methods are very powerful for the detection of genomic variants. Thanks to its throughput and cost-efficiency it enables the detection of a large number of variants in a large number of samples. In this two-day course we will cover the steps from read alignment to variant calling and annotation. We will mainly focus on the detection of germline mutations by following the GATK best practices.
Application deadline: 15 February 2024
The 9th edition of the RNA-seq Data Analysis course will be held on 8-12 April – 2024 in Breda, The Netherlands. This course covers the basic concepts and methods required for RNA-seq analysis. Particular attention is given to the data analysis pipelines for differential transcript expression and variant calling. The course consists of a mixture of lectures and Galaxy, Linux and R practicals. Also the potential of long-read based RNA-seq and AI based analysis enrichments will be explored.
Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the researchers’ needs. This 3-day course will cover the main technologies as well as the main aspects to consider while designing a scRNAseq experiment. In addition, it will cover the theoretical background of analysis methods with hands-on practical data analysis sessions applied to droplet-based methods.
Application deadline: 06 March 2024
The “Python for Beginners” course introduces Python programming, designed for those with little to no prior experience. Upon completion, students will have a firm grasp of Python fundamentals and be equipped with the skills to start their journey in Python programming.
The practical workshop on cleaning your messy data with OpenRefine software.
First, we will cover spreadsheet best practices. Then, we will put that knowledge into practice with OpenRefine. This course will explore the depths of OpenRefine software and see what it can offer. This will include cleaning the data in bigger batches and unifying the data in one sweep (transforms and expressions). Additionally, we will introduce the possibility of downloading additional data from other databases and different extensions OpenRefine software has.
Learning outcomes for the participants:
We ask you to register responsibly. If you can't attend the lecture, please let us know as soon as possible via email (elixir@ut.ee).
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Applications are accepted manually within a few days.
Version control serves as the digital equivalent of a lab notebook. It is employed by professionals to monitor their progress and collaborate effectively. Its utility extends beyond software development; it can be used for books, papers, small datasets, or any evolving content that requires sharing.
Git is a globally adopted tool that helps developers manage changes in collaborative projects. Keeping a record of changes, complete with timestamps and explanations, becomes exceptionally valuable when returning to a project in the future, like a year later when recollection may be unclear.
Learning outcomes for the participants:
We ask you to register responsibly. If you can't attend the lecture, please let us know as soon as possible via email (elixir@ut.ee).
Register: https://forms.gle/QnPtaoWXJevLnhJi8
In order to not miss out on a course next time, subscribe to our newsletter at https://lists.ut.ee/wws/subscribe/elixir.news?previous_action=edit_list_request
Applications are accepted manually within a few days.
On the 25th of May 2023, ELIXIR-Estonia will be organizing a face-to-face data carpentry course in English: Version Control with Git.
Git is used across the world to help developers keep track of changes while working on different parts of the same project. Teams are not the only ones to benefit from version control: lone researchers can benefit immensely. Keeping a record of what was changed, when, and why is extremely useful for all researchers if they ever need to come back to the project later on (e.g., a year later, when memory has faded).
Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Every large software development project relies on it, and most programmers use it for their small jobs as well. And it isn’t just for software: books, papers, small data sets, and anything that changes over time or needs to be shared can and should be stored in a version control system.
Information about the lecture
Date: 25.05.2023
Time: 11:00 - 17:00 (lunch break 12:30-13:30, coffee break 15:00)
City: Tartu
Place: Delta, Narva mnt 18 ROOM 2048
Requirements: Bring your own laptop and install git: https://git-scm.com/downloads
Register: the registration is closed
Prerequisites: In this lesson we use Git from the Unix Shell. Some previous experience with the shell is expected, but isn’t mandatory.
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Learning outcomes:
On the 3rd of March 2023, ELIXIR-Estonia will be organising a face-to-face data management course in English: Basic LINUX/Unix workshop.
This course is aimed to provide basic survival skills in Linux and the terminal environment. We will teach you how to access files and folders, move around and hopefully shake off the fear of getting stuck somewhere along the way.
No prior knowledge is expected.
Information about the lecture
Date: 3.03.2023
Time: 11:00 - 16:00 (lunch break 13:00-14:00)
City: Tallinn
Place: Akadeemia tee 23 ROOM 109
Requirements: Bring your own laptop and please follow the setup tutorial: https://elixirestonia.github.io/2021-09-28-shell-novice/setup.html
Registration is closed.
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Learning outcomes: