1195 materials found

Cellular Microscopy Phenotype Ontology (CMPO): Quick tour

Cellular Microscopy Phenotype Ontology (CMPO): Quick tour from http://www.ebi.ac.uk/training/online/course/cellular-microscopy-phenotype-ontology-cmpo-quick.

Keywords: Ontologies, Cross domain

Cellular Microscopy Phenotype Ontology (CMPO): Quick tour https://tess.elixir-europe.org/materials/cellular-microscopy-phenotype-ontology-cmpo-quick-tour Cellular Microscopy Phenotype Ontology (CMPO): Quick tour from http://www.ebi.ac.uk/training/online/course/cellular-microscopy-phenotype-ontology-cmpo-quick. Ontologies, Cross domain 2016-06-14
BioSamples: Quick tour

BioSamples: Quick tour from http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour.

Keywords: DNA RNA, Gene Expression, Ontologies, Proteins

BioSamples: Quick tour https://tess.elixir-europe.org/materials/biosamples-quick-tour BioSamples: Quick tour from http://www.ebi.ac.uk/training/online/course/biosamples-quick-tour. DNA RNA, Gene Expression, Ontologies, Proteins 2016-06-14
BioSamples Database RDF: webinar

BioSamples Database RDF: webinar from http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar.

Keywords: DNA RNA, Gene Expression, Ontologies, Proteins

BioSamples Database RDF: webinar https://tess.elixir-europe.org/materials/biosamples-database-rdf-webinar BioSamples Database RDF: webinar from http://www.ebi.ac.uk/training/online/course/biosamples-database-rdf-webinar. DNA RNA, Gene Expression, Ontologies, Proteins 2016-06-14
BioModels Database: Quick tour

BioModels Database: Quick tour from http://www.ebi.ac.uk/training/online/course/biomodels-database-quick-tour.

Keywords: Systems

BioModels Database: Quick tour https://tess.elixir-europe.org/materials/biomodels-database-quick-tour BioModels Database: Quick tour from http://www.ebi.ac.uk/training/online/course/biomodels-database-quick-tour. Systems 2016-06-14
Biomedical data: Ethical, legal and social implications

Biomedical data: Ethical, legal and social implications from http://www.ebi.ac.uk/training/online/course/biomedical-data-ethical-legal-and-social-implicati.

Keywords: Cross domain

Biomedical data: Ethical, legal and social implications https://tess.elixir-europe.org/materials/biomedical-data-ethical-legal-and-social-implications Biomedical data: Ethical, legal and social implications from http://www.ebi.ac.uk/training/online/course/biomedical-data-ethical-legal-and-social-implicati. Cross domain 2016-06-14
Biomacromolecular structures: An introduction to EMBL-EBI resources

Biomacromolecular structures: An introduction to EMBL-EBI resources from http://www.ebi.ac.uk/training/online/course/biomacromolecular-structures-introduction-ebi-reso.

Keywords: Proteins

Biomacromolecular structures: An introduction to EMBL-EBI resources https://tess.elixir-europe.org/materials/biomacromolecular-structures-an-introduction-to-embl-ebi-resources Biomacromolecular structures: An introduction to EMBL-EBI resources from http://www.ebi.ac.uk/training/online/course/biomacromolecular-structures-introduction-ebi-reso. Proteins 2016-06-14
Biocuration: An introduction

Biocuration: An introduction from http://www.ebi.ac.uk/training/online/course/biocuration-introduction.

Keywords: Proteins, Cross domain

Biocuration: An introduction https://tess.elixir-europe.org/materials/biocuration-an-introduction Biocuration: An introduction from http://www.ebi.ac.uk/training/online/course/biocuration-introduction. Proteins, Cross domain 2016-06-14
ArrayExpress: Quick tour

This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI...

Scientific topics: Functional genomics, Gene expression and microarray, Gene expression

Keywords: Gene Expression

ArrayExpress: Quick tour https://tess.elixir-europe.org/materials/arrayexpress-quick-tour This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI resources before taking this course. Functional genomics Gene expression and microarray Gene expression Gene Expression Beginners 2016-06-14
Variant-calling

No description available

Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Guide to R swirl interactive lessons

This handout describes how to download the swirl package and start the basic interactive lessons to learn R.

Keywords: R-programming

Guide to R swirl interactive lessons https://tess.elixir-europe.org/materials/guide-to-r-swirl-interactive-lessons This handout describes how to download the swirl package and start the basic interactive lessons to learn R. R-programming
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Statistics and RNA-Seq

This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

Statistics and RNA-Seq https://tess.elixir-europe.org/materials/statistics-and-rna-seq This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Introduction to RNA-seq analysis 2014

This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species.

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

Introduction to RNA-seq analysis 2014 https://tess.elixir-europe.org/materials/introduction-to-rna-seq-analysis-2014 This lecture gives an overview how to perform an RNA-seq experiment. A general RNA-seq workflow is outlined when a good quality genome sequence is available for your species. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
Introduction to R practice codes

These codes give an overview of R object types and programming language structure.

Keywords: R-programming

Introduction to R practice codes https://tess.elixir-europe.org/materials/introduction-to-r-practice-codes These codes give an overview of R object types and programming language structure. R-programming
R/Bioconductor installation and upgrade guide

This handout describes how to download R and install add-on packages, both from CRAN and

Keywords: R-programming

R/Bioconductor installation and upgrade guide https://tess.elixir-europe.org/materials/r-bioconductor-installation-and-upgrade-guide This handout describes how to download R and install add-on packages, both from CRAN and R-programming
RNA-seq training PSB 2013

This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage...

Keywords: Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC

RNA-seq training PSB 2013 https://tess.elixir-europe.org/materials/rna-seq-training-psb-2013 This lecture gives an overview how to perform an RNA-seq experiment. First, the Illumina sequencing platform is briefly covered, followed by the different file formats in NGS. Next, an RNA-seq workflow is outlined, starting from the raw data up to differential expression. The recommended coverage and sequencing mode is touched upon as well as the effect on your analysis of divergence of your genotype compared to the reference. Alignment, Differential-expression, Feature-summarisation, Pre-processing, QC
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
RNA-seq module Bert Overduin

All material concerning RNA-seq analysis

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Pre-processing, QC, Alignment

RNA-seq module Bert Overduin https://tess.elixir-europe.org/materials/rna-seq-module-bert-overduin All material concerning RNA-seq analysis RNA-Seq RNA-Seq, Pre-processing, QC, Alignment
Nicolas Delhomme and Bastian Schiffthaler

This merely lists the various courses at which we taught RNA-Seq data

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

Nicolas Delhomme and Bastian Schiffthaler https://tess.elixir-europe.org/materials/nicolas-delhomme-and-bastian-schiffthaler This merely lists the various courses at which we taught RNA-Seq data RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
Expression estimation

This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed.

Scientific topics: RNA-Seq

Keywords: GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation

Expression estimation https://tess.elixir-europe.org/materials/expression-estimation This introduces how to summarise short read alignments by the annotation of interest to obtain a count-table; i.e. the structure necessary to most downstream expression based analyses. Here, the focus is put on gene-expression, but the aspects of transcript-expression are briefly addressed. RNA-Seq GFF3, BAM, Populus-tremula, RNA-Seq, Expression-estimation
Example “Variant Calling”

No description available

Example “Variant Calling” https://tess.elixir-europe.org/materials/example-variant-calling No description available
Mapping Quality Control

Perform QC on aligned data

Keywords: Alignment, BAM, QC

Mapping Quality Control https://tess.elixir-europe.org/materials/mapping-quality-control Perform QC on aligned data Alignment, BAM, QC
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
Keywords

No description available

Keywords https://tess.elixir-europe.org/materials/keywords No description available
ChIP-Seq

No description available

Keywords: ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation

ChIP-Seq https://tess.elixir-europe.org/materials/chip-seq No description available ChIP-Seq, Experimental-design, QC, ChIP-Seq-QC, Data-format, Alignment, Peak-calling, Differential-binding, Annotation
Tutorial

This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided.

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming

Tutorial https://tess.elixir-europe.org/materials/tutorial This file describes the main tutorial PDF file. Almost all tutorials and hands-on practices are indeed collated in a single document. In addition to this PDF, R code excerpts and installation instructions are also provided. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, R-programming
Prerequisite

No description available

Scientific topics: Statistics and probability

Keywords: Unix, Linux, R-programming, Statistics

Prerequisite https://tess.elixir-europe.org/materials/prerequisite No description available Statistics and probability Unix, Linux, R-programming, Statistics
Intro to R and Bioconductor

R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the...

Keywords: Prerequisite, R-programming

Intro to R and Bioconductor https://tess.elixir-europe.org/materials/intro-to-r-and-bioconductor R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the basic skills that will be needed before using R to analyze NGS data. Prerequisite, R-programming
Preprocessing RNA-Seq data

Quality assessment and preprocessing of RNA-seq data. Description of FastQ format

Keywords: Pre-processing

Preprocessing RNA-Seq data https://tess.elixir-europe.org/materials/preprocessing Quality assessment and preprocessing of RNA-seq data. Description of FastQ format Pre-processing
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

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

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model