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30 materials found

Authors: Jared Simpson  or Vincent Carey  or Tom Freeman  or Eija Korpelainen @eija, eko...  or pajanne 


eQTL / molecular-QTL analyses

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: eQTL / molecular-QTL

eQTL / molecular-QTL analyses https://tess.elixir-europe.org/materials/eqtl-molecular-qtl-analyses Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. eQTL / molecular-QTL
Genetics of gene expression: computation and integrative prediction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: eQTL

Genetics of gene expression: computation and integrative prediction https://tess.elixir-europe.org/materials/genetics-of-gene-expression-computation-and-integrative-prediction Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. eQTL
Visualisation in Statistical Genomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Operations: Visualisation

Visualisation in Statistical Genomics https://tess.elixir-europe.org/materials/visualisation-in-statistical-genomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Scalable Integrative Bioinformatics with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Scalable Computing

Scalable Integrative Bioinformatics with Bioconductor https://tess.elixir-europe.org/materials/scalable-integrative-bioinformatics-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Scalable Computing
eQTL analysis -- an approach with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: eQTL

eQTL analysis -- an approach with Bioconductor https://tess.elixir-europe.org/materials/eqtl-analysis-an-approach-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. eQTL
Lecture: Clustering and classification

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Lecture: Clustering and classification https://tess.elixir-europe.org/materials/lecture-clustering-and-classification Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Statistics and probability
Informatics on High-Throughput Sequencing Data 2018 Module 6-De Novo Assmebly

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads.

Informatics on High-Throughput Sequencing Data 2018 Module 6-De Novo Assmebly https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2018-module-6-de-novo-assmebly Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate students
Informatics on High-Throughput Sequencing Data 2018 Module 1-Introduction to High-Throughput Sequencing

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads.

Informatics on High-Throughput Sequencing Data 2018 Module 1-Introduction to High-Throughput Sequencing https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2018-module-1-introduction-to-high-throughput-sequencing Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Bioinformatics for Cancer Genomics 2018 Module 5-Genome Assembly

Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud.

Bioinformatics for Cancer Genomics 2018 Module 5-Genome Assembly https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2018-module-5-genome-assembly Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Bioinformatics for Cancer Genomics 2018 Module 4-Genome Alignment

Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud.

Bioinformatics for Cancer Genomics 2018 Module 4-Genome Alignment https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2018-module-4-genome-alignment Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Bioinformatics for Cancer Genomics 2017 Module 3-Genome Alignment and Assembly

Course covers the bioinformatics tools required to analyze genomic data sets.

Bioinformatics for Cancer Genomics 2017 Module 3-Genome Alignment and Assembly https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2017-module-3-genome-alignment-and-assembly Course covers the bioinformatics tools required to analyze genomic data sets. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Informatics on High-Throughput Sequencing Data 2017 Module 6-De Novo Assembly

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads.

Informatics on High-Throughput Sequencing Data 2017 Module 6-De Novo Assembly https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2017-module-6-de-novo-assembly Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads. Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Informatics on High-Throughput Sequencing Data 2017 Module 1-Introduction to High-Throughput Sequencing

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads.

Informatics on High-Throughput Sequencing Data 2017 Module 1-Introduction to High-Throughput Sequencing https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-module-1-introduction-to-high-throughput-sequencing Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 6-De Novo Assembly

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 6-De Novo Assembly https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-6-de-novo-assembly Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 1-Introduction to High-Throughput Sequencing

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 1-Introduction to High-Throughput Sequencing https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-1-introduction-to-high-throughput-sequencing Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Post-Doctoral Fellows Researchers Biologists, Genomicists, Computer Scientists
Data Manipulation - Collections: Multisample Analysis

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Tutorial

Data Manipulation - Collections: Multisample Analysis https://tess.elixir-europe.org/materials/data-manipulation-collections-multisample-analysis A collection of microtutorials explaining data manipulation within Galaxy
Data Manipulation - Data: Getting data into Galaxy

A collection of microtutorials explaining data manipulation within Galaxy

Resource type: Slides

Data Manipulation - Data: Getting data into Galaxy https://tess.elixir-europe.org/materials/data-manipulation-data-getting-data-into-galaxy A collection of microtutorials explaining data manipulation within Galaxy
Introduction to Galaxy Analyses - IGV Introduction

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Tutorial

Introduction to Galaxy Analyses - IGV Introduction https://tess.elixir-europe.org/materials/galaxy-introduction-igv-introduction Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Introduction to Galaxy - Multisample Analysis

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Tutorial

Introduction to Galaxy - Multisample Analysis https://tess.elixir-europe.org/materials/galaxy-introduction-multisample-analysis Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Introduction to Galaxy - Getting data into Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Resource type: Slides

Introduction to Galaxy - Getting data into Galaxy https://tess.elixir-europe.org/materials/galaxy-introduction-getting-data-into-galaxy Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Introduction to Galaxy Analyses - Options for using Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which Galaxy instance should I use?

Resource type: Slides

Introduction to Galaxy Analyses - Options for using Galaxy https://tess.elixir-europe.org/materials/galaxy-introduction-options-for-using-galaxy Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which Galaxy instance should I use?
Introduction to Galaxy Analyses - Galaxy 101

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which coding exon has the...

Resource type: Tutorial

Introduction to Galaxy Analyses - Galaxy 101 https://tess.elixir-europe.org/materials/galaxy-introduction-galaxy-101 Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - Which coding exon has the highest number of single nucleotide polymorphisms (SNPs) on human chromosome 22? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Introduction to Galaxy Analyses - From peaks to genes

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get...

Resource type: Tutorial

Introduction to Galaxy Analyses - From peaks to genes https://tess.elixir-europe.org/materials/galaxy-introduction-from-peaks-to-genes Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work
Introduction to Galaxy Analyses - Introduction to Galaxy

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Introduction to Galaxy Analyses - Introduction to Galaxy https://tess.elixir-europe.org/materials/galaxy-introduction-introduction Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Graphical & Computational Modelling of Biological Pathways

Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015

Keywords: Graphical modelling, Roslin Institute

Graphical & Computational Modelling of Biological Pathways https://tess.elixir-europe.org/materials/graphical-computational-modelling-of-biological-pathways-d0b38ce1-0e2e-4ba9-9e0c-39c6af558782 Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015 Graphical modelling, Roslin Institute
An Introduction to BioLayout Express3D

Lecture by professor Tom Freeman. Filmed during a half-day training course held at The Roslin Institute, January 2015, aimed at training biologists with little or no experience of gene expression analysis the basics. Features 15 short films covering the background to data generation through to...

Keywords: Gene expression analysis, Roslin Institute

An Introduction to BioLayout Express3D https://tess.elixir-europe.org/materials/an-introduction-to-biolayout-express3d Lecture by professor Tom Freeman. Filmed during a half-day training course held at The Roslin Institute, January 2015, aimed at training biologists with little or no experience of gene expression analysis the basics. Features 15 short films covering the background to data generation through to deriving meaning using network analysis. - Course aims: the basics of expression data analysis introduction to graph-based analysis introduction to BioLayout Express3D data import navigation of graphs clustering graph analysis data export Gene expression analysis, Roslin Institute
Graphical & Computational Modelling of Biological Pathways

Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015

Keywords: Graphical modelling, Computational modelling, Roslin Institute

Graphical & Computational Modelling of Biological Pathways https://tess.elixir-europe.org/materials/graphical-computational-modelling-of-biological-pathways Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015 Graphical modelling, Computational modelling, Roslin Institute
Material for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis.

Scientific topics: RNA-Seq

Keywords: RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Material for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/material-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. RNA-Seq RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis