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36 materials found

Authors: Eija Korpelainen  or Maria Victoria .  or Julie Sullivan  or Friederike Ehrhart  or nekrut  or Bernardo Clavijo 


Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Single cell RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data

This tutorial how to statistically analyze microarray data with ArrayAnalysis.org website.

Keywords: ArrayAnalysis.org, microarray

How to use the statistics module of ArrayAnalysis.org for statistics analysis of microarray data https://tess.elixir-europe.org/materials/how-to-use-the-statistics-module-of-arrayanalysis-org-for-statistics-analysis-of-microarray-data This tutorial how to statistically analyze microarray data with ArrayAnalysis.org website. ArrayAnalysis.org, microarray post-docs
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions https://tess.elixir-europe.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Transcriptomics, Genomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/rna-seq-data-analysis-using-chipster Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017 Eija Korpelainen Maria Lehtivaara Transcriptomics Genomics transcriptomics, RNA-Seq, eLearning, EeLP Researchers
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
InterMine user tutorial

A tutorial for end users of InterMine

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user tutorial https://tess.elixir-europe.org/materials/intermine-user-tutorial A tutorial for end users of InterMine Data querying, Data analysis, Data download, FAIR Life Science Researchers Bioinformaticians
InterMine user manual

Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine.

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

InterMine user manual https://tess.elixir-europe.org/materials/intermine-user-manual Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine. Data querying, data visualization, Data download, FAIR Life Science Researchers Bioinformaticians
InterMine operator manual

Documentation on how to install, configure and operate an InterMine instance.

Keywords: Data integration, Data analysis, Data publishing, FAIR

Resource type: Documentation

InterMine operator manual https://tess.elixir-europe.org/materials/intermine-operator-manual Documentation on how to install, configure and operate an InterMine instance. Data integration, Data analysis, Data publishing, FAIR Bioinformaticians software engineers
How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping.

Scientific topics: Genetic variation, Genomics

Resource type: Tutorial

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene https://tess.elixir-europe.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. Genetic variation Genomics Biologists
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 - Collections: Using dataset collection

A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections

Resource type: Tutorial

Data Manipulation - Collections: Using dataset collection https://tess.elixir-europe.org/materials/data-manipulation-collections-using-dataset-collection A collection of microtutorials explaining data manipulation within Galaxy Questions of the tutorial: - How to manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections
User Interface and Features - Histories: Understanding Galaxy history system

A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories

Resource type: Tutorial

User Interface and Features - Histories: Understanding Galaxy history system https://tess.elixir-europe.org/materials/user-interface-and-features-histories-understanding-galaxy-history-system A collection of microtutorials explaining various features of the Galaxy user interface Questions of the tutorial: - How do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories
Assembly - Making sense of a newly assembled genome

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Making sense of a newly assembled genome https://tess.elixir-europe.org/materials/assembly-making-sense-of-a-newly-assembled-genome DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I just assembled a genome. How does it compare with already sequenced genomes? - How do I find rearranged, inserted, or deleted regions? Objectives of the tutorial: - Identification of the most closely related genome to my new assembly - Perform sequence comparison to locate rearrangements - Identify genes located in deletions
Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé

This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online.

Keywords: nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé

Resource type: Tutorial

Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé https://tess.elixir-europe.org/materials/browsing-the-enanomapper-ontology-with-bioportal-aberowl-and-protege This tutorial explains how the eNanoMapper ontology can be browsed with three tools, of which two are online. nanotoxicology, Ontologies, BioPortal, AberOWL, Protégé PhD students post-docs
Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

Resource type: course materials, Video

Community analysis of amplicon sequencing data (16S rRNA) https://tess.elixir-europe.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

Virus detection using small RNA-seq https://tess.elixir-europe.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

Scientific topics: RNA-Seq

Resource type: course materials, Video

RNA-seq data analysis https://tess.elixir-europe.org/materials/rna-seq-data-analysis-with-chipster This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
Metagenomics data analysis

This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...

Scientific topics: Metagenomics

Resource type: Video, course materials

Metagenomics data analysis https://tess.elixir-europe.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics
Variant Analysis - Calling very rare variants

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What frequency of variants is so low that it is obscured by sequencing error rate? - What are the different types of consensus sequences produced from duplex sequencing? Objectives of...

Resource type: Tutorial

Variant Analysis - Calling very rare variants https://tess.elixir-europe.org/materials/variant-analysis-calling-very-rare-variants Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - What frequency of variants is so low that it is obscured by sequencing error rate? - What are the different types of consensus sequences produced from duplex sequencing? Objectives of the tutorial: - Processing raw duplex sequencing data into consensus sequences - Find rare variants without relying on diploid assumptions
Variant Analysis - Calling variants in diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to find variable sites in diploid genomes? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in human genome.

Resource type: Tutorial

Variant Analysis - Calling variants in diploid systems https://tess.elixir-europe.org/materials/variant-analysis-calling-variants-in-diploid-systems Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How to find variable sites in diploid genomes? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in human genome.
Variant Analysis - Calling variants in non-diploid systems

Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How does frequency of mitochondrial polymorphisms change from mother to child? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in bacteria,...

Resource type: Tutorial

Variant Analysis - Calling variants in non-diploid systems https://tess.elixir-europe.org/materials/variant-analysis-calling-variants-in-non-diploid-systems Exome sequencing means that all protein-coding genes in a genome are sequenced Questions of the tutorial: - How does frequency of mitochondrial polymorphisms change from mother to child? Objectives of the tutorial: - Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles.
Introduction to Galaxy Analyses - NGS data logistics

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 manipulate and process...

Resource type: Tutorial

Introduction to Galaxy Analyses - NGS data logistics https://tess.elixir-europe.org/materials/introduction-to-galaxy-ngs-data-logistics 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 manipulate and process NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.
Introduction to Galaxy - Understanding Galaxy history system

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 do Galaxy histories...

Resource type: Tutorial

Introduction to Galaxy - Understanding Galaxy history system https://tess.elixir-europe.org/materials/introduction-to-galaxy-understanding-galaxy-history-system 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 do Galaxy histories work? Objectives of the tutorial: - Gain understanding on navigating and manipulating histories
Transcriptomics - Reference-based RNAseq data analysis (long)

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis

Resource type: Tutorial

Transcriptomics - Reference-based RNAseq data analysis (long) https://tess.elixir-europe.org/materials/transcriptomics-reference-based-rnaseq-data-analysis-long Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis
Assembly - Unicycler Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Resource type: Tutorial

Assembly - Unicycler Assembly https://tess.elixir-europe.org/materials/assembly-unicycler-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - I have short reads and long reads. How do I assemble a genome? Objectives of the tutorial: - Perform Quality Control on your reads - Perform a Small genome Assembly with Unicycler - Evaluate the Quality of the Assembly with Quast - Annotate the assembly with Prokka
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 - Using dataset collection

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 manipulate large numbers...

Resource type: Tutorial

Introduction to Galaxy - Using dataset collection https://tess.elixir-europe.org/materials/galaxy-introduction-collections 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 manipulate large numbers of datasets at once? Objectives of the tutorial: - Understand and master dataset collections
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
Genome assembly and validation

Course materials from the 2015 de novo course.

Keywords: Earlham Institute

Genome assembly and validation https://tess.elixir-europe.org/materials/genome-assembly-and-validation Course materials from the 2015 de novo course. Earlham Institute