Register training material
45 materials found

Content provider: Bioinformatics and Biomathe... 


Train the trainer

Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics Training hub. The five slide decks cover pedagogical theory, trainer...

Scientific topics: Computational biology, Bioinformatics

Keywords: training, pedagogy

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

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

Docker version of Welsh Gene Park NGS course

Welcome to the IFR Dockerised version of the Welsh Genepark's
Introduction to Command-line NGS Analysis course!
The original materials belong to Wesh Genepark and the original
materials and software can be found here.

This...

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

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

Welcome to the IFR Dockerised version of the Welsh Genepark's
Introduction to Command-line NGS Analysis course!
The original materials belong to Welsh Genepark and the original
materials and software can be found here.

This...

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

Phylogenetics & Phylogeography (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography (lecture-part 1)

  2. Phylogenetics & Phylogeography (lecture-part 2)

  3. Phylogenetics & Phylogeography (lecture-part 3)

  4. Phylogenetics & Phylogeography (lecture-part 4)

  5. Phylogenetics & Phylogeography (lecture-part 5)

6....

Keywords: Phylogenetics, Roslin Institute

Molecular epidemiology practical

  1. Molecular epidemiology - practical 1

  2. Molecular epidemiology - practical 1 review

  3. Molecular epidemiology - practical 2 part 1

  4. Molecular epidemiology - practical 2 part 2

  5. Molecular epidemiology - practical 2 review

  6. Molecular epidemiology - practical 3 part 1

7....

Keywords: Molecular epidemiology, Roslin Institute

Phylogenetic analysis of pathogens: Staphylococcus aureus, host switching and antibiotic resistance

  1. Phylogenetic analysis of pathogens (lecture - part1)

  2. Phylogenetic analysis of pathogens (lecture - part2)

  3. Phylogenetic analysis of pathogens (lecture - part3)

  4. Phylogenetic analysis of pathogens (lecture - part4)

  5. Phylogenetic analysis of pathogens (lecture - part5)

6....

Keywords: Phylogenetic analysis, Roslin Institute

Graphical & Computational Modelling of Biological Pathways

  1. Introduction

  2. Many Views of A Pathway(Lecture)

  3. Pathway Models & Pathway Types (Lecture)

  4. Sources of ‘Pathway Data’ (Lecture)

  5. Issues (Lecture)

  6. SBGN (Lecture)

  7. mEPN (Lecture)

  8. Practical Session: Pathway to Pathway Construction - yED(1)

  9. Practical...

Keywords: Graphical modelling, Roslin Institute

An Introduction to BioLayout Express3D

1.Introduction to data analysis - course overview (lecture)

2.Introduction to networks (lecture)

  1. BioLayout Express3D - background and benefits (lecture)

  2. BioLayout Express3D – getting started 1 (Practical Session)

  3. BioLayout Express3D – getting started 2 (Practical...

Keywords: Gene expression analysis, Roslin Institute

Phylogenetics & Phylogeography Practical (Advanced Analytical Methods)

  1. Phylogenetics & Phylogeography Practical - Overview

  2. Phylogenetics & Phylogeography Practical 1

  3. Phylogenetics & Phylogeography Practical 2 - Part 1

  4. Phylogenetics & Phylogeography Practical 2 - Part 2

  5. Phylogenetics & Phylogeography Practical 3

6....

Keywords: Phylogenetics, Phylogeography, Roslin Institute

Graphical & Computational Modelling of Biological Pathways

  1. Introduction

  2. Many Views of A Pathway(Lecture)

  3. Pathway Models & Pathway Types (Lecture)

  4. Sources of ‘Pathway Data’ (Lecture)

  5. Issues (Lecture)

  6. SBGN (Lecture)

  7. mEPN (Lecture)

  8. Practical Session: Pathway to Pathway Construction - yED(1)

  9. Practical...

Keywords: Graphical modelling, Computational modelling, Roslin Institute

SAS Introduction

1.Introduction

  1. Data summary

  2. Demo – Data Summary

  3. Demo – Data Summary cont.

  4. Data summary using PROC TABULATE and PROC GPLOT

  5. Statistical analysis

  6. Example analysis

  7. Example analysis cont.1

  8. Example analysis cont.2

  9. Reading and manipulating...

Keywords: SAS, Roslin Institute

A Brief Introduction to R

  1. A Brief Introduction to R

  2. Very Basic Functions

  3. Demo Data - Rivers

  4. Demo Data - Rivers (Cont.)

  5. Demo Data - Orange

  6. Demo Data - Orange (Cont.)

  7. Demo data - Anderson's Iris Data

  8. Demo Data - US Judge Rating

  9. Summary

Keywords: R language, Roslin Institute

Summarising Data

  1. Introduction

  2. Introduction to Data Summary & Types of data

  3. Continuous Data – Measures of Location

  4. Continuous Data – Measures of Spread & Accuracy

  5. Continuous Data with Skewed or Odd Distributions – Measures of Spread

  6. Choosing Appropriate Summary Statistics...

Keywords: Summarising data, Roslin Institute

Basic Statistical Tests

  1. Introduction

  2. Hypothesis Testing

  3. Choosing Between Parametric & Non-Parametric Tests

  4. T-Test for Comparing Two Groups

  5. T-Test – Interpreting Software Output

  6. Paired T-Test

  7. Mann-Whitney U-Test to Compare Two Groups When Data Are Not Normally Distributed

8....

Keywords: Statistical tests, Roslin Institute

Introduction to Experimental Design

  1. Introduction

  2. Achieving Statistical Significance

  3. Achieving Generalisable Results

  4. Avoiding Bias

  5. Questions to Address When Planning

  6. Examples of Experimental Designs

  7. Randomised Block Design

  8. Crossover & Repeated Measures Designs

  9. Pilot & Proof...

Keywords: Experimental design, Roslin Institute

Introduction to Sample Size Calculation

  1. Introduction

  2. Sample Size Calculation – Basic Formula

  3. Example 1

  4. Calculating In Terms of ‘Difference to Detect’ & Power From Sample Size

  5. Example 2

  6. Different Numbers Per Group

  7. Different Variances for Groups

  8. Binary Data

  9. Allowing for...

Keywords: Sample size, Roslin Institute

Introduction to Statistical Modelling

  1. Introduction

  2. One-Way Analysis of Variance (ANOVA) Recap

  3. Two-Way ANOVA - Assessing Two Effects in Same Model

  4. Two-Way ANOVA - Allowing for Structure in The Data

  5. Paired T-Test Using Two-Way ANOVA & ANOVA With More Effects

  6. Regression Recap

  7. General Linear...

Keywords: Statistical modelling, Roslin Institute

Introduction to Mixed Models

  1. Introduction

  2. What Are Mixed Models?

  3. Potential Advantages of Mixed Models

  4. Historical Perspective

  5. Example 1: Biological & Technical Replicates

  6. Example 2: Rabbit Inspiration Time – Sources of Variation

  7. Non-Normal Data

  8. Example 3: Non-normal data

9....

Keywords: Mixed models, Roslin Institute

Introduction to Analysing Repeated Measures Data

  1. Introduction

  2. Potential Analysis Approaches

  3. Mixed Model Analysis

  4. Covariance Pattern Model

  5. Example – Covariance Pattern Model

  6. Significance Testing for Fixed Effects

  7. Model Checking

  8. Random Coefficients (Slopes) Models

  9. Example – Random Coefficients...

Keywords: Data analysis, Repeated measures, Roslin Institute

Quality Control in Sequencing Experiments

This course looks at the different ways in which sequencing based studies can fail and the options for visualisation and QC which allow you to identify and diagnose these failures at an early stage. It is designed to be of use to anyone who is using sequencing as part of their research, not just...

Scientific topics: Quality affairs

Keywords: Babraham Institute

Extracting biological information from gene lists

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting...

Keywords: Functional analysis, Gene lists, Babraham Institute

Sample size estimation

Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with...

Keywords: Power analysis, Sample size, Babraham Institute

Statistical Analysis using SPSS

Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.

Course Content

*...

Scientific topics: Statistics and probability

Keywords: Babraham Institute

Statistical Analysis using GraphPad Prism

GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.

Course Content

*...

Keywords: GraphPad Prism, Babraham Institute

Scientific Figure Design

This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and...

Scientific topics: Data visualisation

Keywords: Figure design, Babraham Institute

An Introduction to Unix

Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this.

This course provides an introduction to the concepts of unix and provides a...

Keywords: Unix, Babraham Institute

An Introduction to ggplot

Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs.

**Course...

Keywords: ggPlot, Babraham Institute

Plotting complex figures with R

This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding...

Keywords: Graph plotting, R Programming, Babraham Institute