PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to biological data science. This online workshop is taught by experienced Edinburgh Genomics’ trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types and structures. We then move on to using functions, introducing a selection of packages for biological data science. Finally, we will learn how to visualise your data to generate publication-ready plots using the package ggplot2.

Instructors

• Nathan Medd (Training and Outreach Manager)
• Heleen De Weerd (Bioinformatician)

Workshop format

The workshop consists of presentations and hands-on tutorials.

Who should attend

Undergraduates, Graduates, postgraduates, and PIs, who are using, or planning to use, the statistical software R to manipulate and analyse biological data in their research. This is an introductory level course: no prior experience of R (or any other programming language) is necessary before starting the workshop.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to biological data science. This online workshop is taught by experienced Edinburgh Genomics’ trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types and structures. We then move on to using functions, introducing a selection of packages for biological data science. Finally, we will learn how to visualise your data to generate publication-ready plots using the package ggplot2.

Instructors

• Nathan Medd (Training and Outreach Manager)
• Heleen De Weerd (Bioinformatician)

Workshop format

The workshop consists of presentations and hands-on tutorials.

Who should attend

Undergraduates, Graduates, postgraduates, and PIs, who are using, or planning to use, the statistical software R to manipulate and analyse biological data in their research. This is an introductory level course: no prior experience of R (or any other programming language) is necessary before starting the workshop.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

This course aims to provide an introduction to the principles of short variant discovery (both germline and somatic) from short-read data. We will look at a complete workflow, from data QC to functional interpretation of variant calls. The practical sessions will focus on running the GATK pipeline from the Broad Institute.

Instructors: Frances Turner & the Edinburgh Genomics Bioinformatics Team

Venue: Online

Requirements:

This course is intended for researchers who need to analyse genomic data in order to call genomic variants. Aside from a basic understanding of molecular biology, attendees must have a working knowledge of how to use the Linux BASH command line - our 1-day "Linux for bioinformatics" course is a suitable background.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

Edinburgh Genomics: RNA-seq Data Analysis

RNA sequencing (RNA-seq) has become the method of choice for transcriptome profiling. Nevertheless, it is a non-trivial task to transform the vast amount of data obtained with high-throughput sequencers into useful information. Thus, RNA-seq data analysis is still a major bottleneck for most researchers in this field. The ability to correctly interpret RNA-seq results, as well as knowledge of the intrinsic properties of these data, are essential to avoid incorrect experimental designs and the application of inappropriate analysis methodologies. The aim of this workshop is to familiarise researchers with RNA-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs will be used.

Instructors: Urmi Trivedi, Frances Turner, Nathan Medd 

Workshop format

The workshop consists of presentations and hands-on tutorials.

Who should attend

Graduates, postgraduates, and PIs, who are using, or planning to use, RNA-seq technology in their research and want to learn how to process and analyse RNA-seq data.

Requirements

A general understanding of molecular biology and genomics. A

An image is more than a pretty picture.  It contains data that can be extracted and quantified.  During the five half-day course, students learn about the structure of an image –what a good image is- as well as different techniques to extract data in 2d, over time and in 3D.  The software that we’ll use are all freeware: Fiji, Ilastik, CellProfiler. 

Students get typical images, course notes and access to recording.

Instructors: Matthieu Vermeren

Please give me the name of your PI and the Centre/institute where you are working. Bonus points to those that give their grant number! 

Pre-requisites: You will need to install the following software:
1. Fiji (https://imagej.net/software/fiji/).
2. Ilastik (https://www.ilastik.org/)
3. CellProfiler and CellProfiler Analyst (https://cellprofiler.org/)

NOTE: You may need to ask IS/administrator for permission. 
NOTE 2: We are using FIJI, which has extra functionalities over ImageJ. Make sure you install Fiji.
Course material in form of test files and detailed booklets will be provided.

Location: wherever you have access to a computer and a good internet.

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

Edinburgh Genomics: Introduction to Linux for Genomics

Genomic studies produce vast amounts of data, usually in the form of very large text files. Linux is particularly suited to working with such files, and is therefore arguably one of the most important tools in a bioinformatician’s toolkit. The Linux command-line enables one to view,
filter and manipulate large text files that are difficult or impossible to handle with applications like Word or Excel, write pipelines to mperform certain tasks, and run bioinformatics software for which no web interface is available. In this workshop, we will first cover the most used Linux commands, followed by a short introduction to several popular command-line tools that were specially developed for genomics as well as file formats commonly used in genomics (BED, FASTA, FASTQ, GFF/GTF, SAM/BAM, VCF).

Instructors:Tim Booth & Nathan Medd

Workshop format
The workshop consists of guided tutorials and hands-on exercises. Roughly 3/4 of the workshop will be spent on Linux and 1/4 on command-line tools for genomics and file formats.

Who should attend
Graduates, postgraduates, and PIs, without any previous command-line experience.

Requirements
A general understanding of molecular biology and genomics and elementary skills in computer usage are required. A computer with stable internet connection and small VNC viewer software (download instructions included)