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Course at Bern, Switzerland: NGS - Genome Variant Analysis

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

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Course at Breda, The Netherlands: RNA-seq data analysis

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.

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Course at Bern, Switzerland: Single-Cell Transcriptomics with R

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

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Course at EMBL-EBI: Summer school in bioinformatics

European Bioinformatics Institute United Kingdom in association with Elixir Estonia are organising summer school in bioinformatics. This course provides an introduction to the use of bioinformatics in biological research, giving you guidance for using bioinformatics in your work whilst also providing hands-on training in tools and resources appropriate to your research.

Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their knowledge and skills further. No previous knowledge of programming is required for this course.

Applications close: 25 February 2024

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  • 1 min read

Genoomika taristu arengusuundadest Euroopas ja Eestis

Presentation about the directions of Genomic Infrastructure in Europe and Estonia by Hedi Peterson. The presentation took place at the annual conference of Estonian Human Genetics Association in Rakvere, October 19th, 2023.

Andmekaitse ja infoturve teadustöös/Data protection in research

ENGLISH BELOW

Avatud teadus Eestis kutsub avatud juurdepääsu nädalal (23-27.10) teadlasi, doktorante, teadusadministraatoreid, raamatukoguhoidjaid ja teisi huvilisi veebiseminarile: „Andmekaitse ja infoturve teadustöös“. Üritus toimub 25.10. kell 13.00-14.30 Zoomi keskkonnas.
Veebiseminaril on kolm ettekannet, millest kaks on eesti keelsed ning üks inglise keelne.
Veebiseminaril tutvustatakse juhendit „Andmekaitse teadustöös“ (Marten Juurik, ETAG/TÜ), infoturvet ning selle seost teadustööga (Toomas Lepik, TalTech) ja anonümiseerimistööriista Amnesia (Manolis Terrovitis, OpenAIRE – inglise keeles algusega kell 14.00).

registreeri: https://ut-ee.zoom.us/meeting/register/tJ0pfu2uqD0uHNEbGMM6wOZxryLRiITOMaio#/registration

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During the Open Access Week (23-27.10), Open Science in Estonia invites researchers, doctoral students, research administrators, librarians, and other interested parties to a webinar „Data protection in Research“. The event will take place on 25.10. from 13:00 to 14:30 in the Zoom environment. The webinar will feature three presentations, two of which will be in Estonian, and one in English. The presentations will cover the following topics: Introduction to the "Data Protection in Research" guide (Marten Juurik, ETAG/UT), information security and its relevance to research (Toomas Lepik, TalTech) and introduction to the anonymization tool, Amnesia (Manolis Terrovitis, OpenAIRE – starting at 14:00 in English). Event will be recorded and shared through UT DSpace.

Register: https://ut-ee.zoom.us/meeting/register/tJ0pfu2uqD0uHNEbGMM6wOZxryLRiITOMaio#/registration

Autumn semester ELIXIR courses

ELIXIR Estonia is continuing with the data management-related lectures and workshops this semester. To get more information about these courses, read below and visit https://elixir.ut.ee/training.  

 

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).

 

How to make your messy data usable? / OpenRefine - 30.11.2023

  • Time: 30.11.2023 13:00-17:00
  • Type: Workshop
  • Language: English
  • Duration: 4h
  • Location: Delta building, Narva mnt 18 room 1008, Tartu
  • Audience: People, who need to clean messy data
  • Instructor: Diana Pilvar, MSc

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: 

  • Describe spreadsheet best practices
  • Compare Excel and OpenRefine
  • Apply transforms (cell editing, column editing, transposing) in OpenRefine
  • Write simple expressions in OpenRefine
  • Match your dataset with that of an external source 

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).

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.