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12 materials found

Authors: Malachi Griffith  or Tuur Muyldermans 


Containers & Workflow pipelines workshop

The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify...

Keywords: Containers, Nextflow

Resource type: Training materials

Containers & Workflow pipelines workshop http://tess.elixir-uk.org/materials/containers-workflow-pipelines-workshop The first day (20 May 2021) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers. After an extensive explanation on Docker containers, at the end of the first day, Singularity will be highlighted as well. On the second day (27 May 2021), you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step, all in the new DSL2 language. Containers, Nextflow bioinformaticians
Introduction to Nextflow workshop

workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available...

Scientific topics: Workflows

Keywords: Nextflow, DSL2

Resource type: Presentation, course materials

Introduction to Nextflow workshop http://tess.elixir-uk.org/materials/introduction-to-nextflow-workshop workshop materials (mainly) in DSL2 aiming to get familiar with the Nextflow syntax by explaining basic concepts and building a simple RNAseq pipeline. Highlights also reproducibility aspects with adding containers (docker & singularity). Slides available [here](https://github.com/vibbits/nextflow-jnj/blob/master/presentation/slidedeck.pdf) Workflows Nextflow, DSL2 bioinformaticians
Reproducible data analysis with RStudio, github and Rmarkdown

Best practices for writing reproducible data-analysis Creating a reproducible and re-usable data-analysis environment with Rstudio Input: https://github.com/vibbits/RDM-LS Output: https://github.com/vibbits/RDM-LS-solution

Scientific topics: Data management, Data architecture, analysis and design

Keywords: Data analysis

Resource type: Presentation

Reproducible data analysis with RStudio, github and Rmarkdown http://tess.elixir-uk.org/materials/reproducible-data-analysis-with-rstudio-github-and-rmarkdown Best practices for writing reproducible data-analysis Creating a reproducible and re-usable data-analysis environment with Rstudio Input: https://github.com/vibbits/RDM-LS Output: https://github.com/vibbits/RDM-LS-solution Data management Data architecture, analysis and design Data analysis life scientists
Research Data Management in Life Sciences

The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences.

Scientific topics: Data management

Resource type: Presentation, Vignette, Video

Research Data Management in Life Sciences http://tess.elixir-uk.org/materials/research-data-management-in-life-sciences The content provided via this link was used in the training on 9 and 10 November 2020 organized by Ghent University and Elixir Belgium and VIB in collaboration with Interreg Vlaanderen-Nederland: https://training.vib.be/all-trainings/research-data-management-life-sciences. Data management Life Science Researchers
Informatics for RNA-Seq Analysis 2018 Module 4-Reference Free Alignment

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 4-Reference Free Alignment http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2018-module-4-reference-free-alignment Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
Informatics for RNA-Seq Analysis 2018 Module 1-Introduction to RNA Sequencing Analysis

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2018 Module 1-Introduction to RNA Sequencing Analysis http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2018-module-1-introduction-to-rna-sequencing-analysis Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Biologists, Genomicists, Computer Scientists Graduate students Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 5-Isoform Discovery and Alternative Expression

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 5-Isoform Discovery and Alternative Expression http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-5-isoform-discovery-and-alternative-expression Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 4-Reference Free Alignment

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 4-Reference Free Alignment http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-4-reference-free-alignment Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate Students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Informatics for RNA-Seq Analysis 2017 Module 1-Introduction to RNA Sequencing Analysis

Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages.

Informatics for RNA-Seq Analysis 2017 Module 1-Introduction to RNA Sequencing Analysis http://tess.elixir-uk.org/materials/informatics-for-rna-seq-analysis-2017-module-1-introduction-to-rna-sequencing-analysis Course providing an introduction to RNA-seq data analysis followed by integrated tutorials demonstrating the use of popular RNA-seq analysis packages. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
High-Throughput Biology 2017 Module 11-Isoform Discovery and Alternative Expression

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 11-Isoform Discovery and Alternative Expression http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-11-isoform-discovery-and-alternative-expression Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate Students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 10-Reference Free Alignment

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 10-Reference Free Alignment http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-10-reference-free-alignment Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 7-Introduction to RNA Sequencing Analysis

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 7-Introduction to RNA Sequencing Analysis http://tess.elixir-uk.org/materials/high-throughput-biology-2017-module-7-introduction-to-rna-sequencing-analysis Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows