Register training material
35 materials found

Node: United Kingdom 

and

Keywords: Exploratory-analysis  or metagenomics  or Roslin Institute  or Institute of Food Research 


Bioinformatics and Virtual Machines

We introduce the concept of the virtual machine, what they can be used for and the advantages and disadvantages of using them.

Keywords: VM, IFR, Institute of Food Research, Quadram Institute, Bioinformatics

Bioinformatics and Virtual Machines https://tess.elixir-europe.org/materials/bioinformatics-and-virtual-machines We introduce the concept of the virtual machine, what they can be used for and the advantages and disadvantages of using them. VM, IFR, Institute of Food Research, Quadram Institute, Bioinformatics
LXDE RStudio with support for bioconductor tools

An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation

Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute

LXDE RStudio with support for bioconductor tools https://tess.elixir-europe.org/materials/lxde-rstudio-with-support-for-bioconductor-tools An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation RNA-Seq, IFR, Institute of Food Research, Quadram Institute
IFR Dockerised version of the EBI's Introduction to RNA-seq course

This is basically the EBI RNA-seq course bundled up in a Docker container using LXDE via TightVNC to provide a graphical environment. The material has been repackaged to use an Ipython Notebook as the learning environment which can be annotated by the learner.

Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute

IFR Dockerised version of the EBI's Introduction to RNA-seq course https://tess.elixir-europe.org/materials/ifr-dockerised-version-of-the-ebi-s-introduction-to-rna-seq-course This is basically the EBI RNA-seq course bundled up in a Docker container using LXDE via TightVNC to provide a graphical environment. The material has been repackaged to use an Ipython Notebook as the learning environment which can be annotated by the learner. RNA-Seq, IFR, Institute of Food Research, Quadram Institute
Docker version of Welsh Gene Park NGS course

Docker version of Welsh Gene Park NGS course

Keywords: NGS, IFR, Institute of Food Research, Quadram Institute

Docker version of Welsh Gene Park NGS course https://tess.elixir-europe.org/materials/docker-version-of-welsh-gene-park-ngs-course Docker version of Welsh Gene Park NGS course NGS, IFR, Institute of Food Research, Quadram Institute
IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis

The IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis course

Keywords: NGS, Command line, IFR, Institute of Food Research, Quadram Institute

IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis https://tess.elixir-europe.org/materials/ifr-dockerised-version-of-the-welsh-genepark-s-introduction-to-command-line-ngs-analysis The IFR Dockerised version of the Welsh Genepark's Introduction to Command-line NGS Analysis course NGS, Command line, IFR, Institute of Food Research, Quadram Institute
Phylogenetics & Phylogeography (Advanced Analytical Methods)

Phylogenetics and Phylogeography(Advanced Analytical Methods) Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetics, Roslin Institute

Phylogenetics & Phylogeography (Advanced Analytical Methods) https://tess.elixir-europe.org/materials/phylogenetics-phylogeography-advanced-analytical-methods Phylogenetics and Phylogeography(Advanced Analytical Methods) Lecture by Dr Sam Lycett, filmed at The Roslin Institute, March 2015. Phylogenetics, Roslin Institute
Molecular epidemiology practical

Practical session with Dr. Emily Richardson, filmed at The Roslin Institute, March 2015.

Keywords: Molecular epidemiology, Roslin Institute

Molecular epidemiology practical https://tess.elixir-europe.org/materials/molecular-epidemiology-practical Practical session with Dr. Emily Richardson, filmed at The Roslin Institute, March 2015. Molecular epidemiology, Roslin Institute
Phylogenetic analysis of pathogens: Staphylococcus aureus, host switching and antibiotic resistance

Lecture by professor Ross Fitzgerald, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetic analysis, Roslin Institute

Phylogenetic analysis of pathogens: Staphylococcus aureus, host switching and antibiotic resistance https://tess.elixir-europe.org/materials/phylogenetic-analysis-of-pathogens-staphylococcus-aureus-host-switching-and-antibiotic-resistance Lecture by professor Ross Fitzgerald, filmed at The Roslin Institute, March 2015. Phylogenetic 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, 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
Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015.

Keywords: Phylogenetics, Phylogeography, Roslin Institute

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods) https://tess.elixir-europe.org/materials/phylogenetics-phylogeography-practical-advanced-analytical-methods Practical session with Dr Sam Lycett, filmed at The Roslin Institute, March 2015. Phylogenetics, Phylogeography, 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
SAS Introduction

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, April 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: SAS, Roslin Institute

SAS Introduction https://tess.elixir-europe.org/materials/sas-introduction Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, April 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. SAS, Roslin Institute
A Brief Introduction to R

A short training session with Dr. Ian Handel at The Roslin Institute, April 2015

Keywords: R language, Roslin Institute

A Brief Introduction to R https://tess.elixir-europe.org/materials/a-brief-introduction-to-r A short training session with Dr. Ian Handel at The Roslin Institute, April 2015 R language, Roslin Institute
Summarising Data

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Summarising data, Roslin Institute

Summarising Data https://tess.elixir-europe.org/materials/summarising-data Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Summarising data, Roslin Institute
Basic Statistical Tests

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Statistical tests, Roslin Institute

Basic Statistical Tests https://tess.elixir-europe.org/materials/basic-statistical-tests Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Statistical tests, Roslin Institute
Introduction to Experimental Design

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Experimental design, Roslin Institute

Introduction to Experimental Design https://tess.elixir-europe.org/materials/introduction-to-experimental-design Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Experimental design, Roslin Institute
Introduction to Sample Size Calculation

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. A spreadsheet...

Keywords: Sample size, Roslin Institute

Introduction to Sample Size Calculation https://tess.elixir-europe.org/materials/introduction-to-sample-size-calculation Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, January 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. A spreadsheet to carry out the calculations described in the presentation may be copied here: http://datashare.is.ed.ac.uk/handle/10283/1996 Sample size, Roslin Institute
Introduction to Statistical Modelling

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Statistical modelling, Roslin Institute

Introduction to Statistical Modelling https://tess.elixir-europe.org/materials/introduction-to-statistical-modelling Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Statistical modelling, Roslin Institute
Introduction to Mixed Models

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Mixed models, Roslin Institute

Introduction to Mixed Models https://tess.elixir-europe.org/materials/introduction-to-mixed-models Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Mixed models, Roslin Institute
Introduction to Analysing Repeated Measures Data

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Data analysis, Repeated measures, Roslin Institute

Introduction to Analysing Repeated Measures Data https://tess.elixir-europe.org/materials/introduction-to-analysing-repeated-measures-data Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Data analysis, Repeated measures, Roslin Institute
Introduction to ChIP-Seq Using Galaxy: Analysing protein interactions with DNA

ChIP-sequencing, also known as ChIP-Seq, is a powerful technique for investigating protein interactions with DNA. This course will take you through an example ChIP-Seq analysis pipeline, following a published methodology to show how we can understand and reproduce these published results.

Scientific topics: ChIP-seq

Keywords: Roslin Institute

Introduction to ChIP-Seq Using Galaxy: Analysing protein interactions with DNA https://tess.elixir-europe.org/materials/introduction-to-chip-seq-using-galaxy-analysing-protein-interactions-with-dna ChIP-sequencing, also known as ChIP-Seq, is a powerful technique for investigating protein interactions with DNA. This course will take you through an example ChIP-Seq analysis pipeline, following a published methodology to show how we can understand and reproduce these published results. ChIP-seq Roslin Institute Any student, postdoc or RA who has an interest in bioinformatics and who intends to conduct ChIP-Seq analysis on a Galaxy platform.
RNA-seq module Frederik Coppens

Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.

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

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128 Material concerning RNA-seq analysis, with an emphasis on the statistical aspects. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
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
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
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
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
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
Material provided by Charlotte Soneson

This folder contains material provided by Charlotte Soneson. The following material is included:

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis