Please sign up Here before paying for this face to face course

Edinburgh Genomics: Introduction to Python for Biologists

Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way.

Instructor:

Tim Booth, Nathan Medd

Course Developer:
Dr. Martin Jones (Founder, Python for Biologists)

Workshop format
Five days. See web page for details 

Who should attend

See web page for details 

Requirements

See web page for details 

The workshop will be held in person not online, you will be emailed details once you have registered.

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

Single cell RNA-Seq offers many advantages over bulk RNA-Seq, but the richer data produced requires a more complex analysis. In this course we will learn about the advantages of single cell sequencing, and when it may be an appropriate choice, how to perform common types of data analysis, and to spot and deal with potential problems.  We will analyse 10X genomics data with the R package Seurat.

Who this course is for

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 working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop.
• A working knowledge of R at the level of Edinburgh Genomics R for Biologists workshop.
  (If you are unsure of how these relate to your coding skills please check the above course pages and look at topics covered)

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

Single cell RNA-Seq offers many advantages over bulk RNA-Seq, but the richer data produced requires a more complex analysis. In this course we will learn about the advantages of single cell sequencing, and when it may be an appropriate choice, how to perform common types of data analysis, and to spot and deal with potential problems.  We will analyse 10X genomics data with the R package Seurat.

Who this course is for

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 working knowledge of Linux at the level of the Edinburgh Genomics Linux for Genomics workshop.
• A working knowledge of R at the level of Edinburgh Genomics R for Biologists workshop.
  (If you are unsure of how these relate to your coding skills please check the above course pages and look at topics covered)

PLEASE SIGN UP HERE BEFORE PAYING FOR THIS COURSE

Edinburgh Genomics: Illumina 

In this course you will learn how to produce whole genome sequencing libraries using the new RNA library preparation kits from Illumina, which provide a quick and simple work-flow for library production. You will get to work on both a high-quality training sample and have the opportunity to bring your own RNA sample for library preparation and sequencing. This course assumes you have a basic level of laboratory experience in a molecular biology lab, although experienced demonstrators will always be on hand to guide you. If you have limited lab experience, please indicate this on the registration form and we will try to accommodate you.imple work-flow for library production. More detailed description of the session can be found on the pdf you receive when signing up.

Who should attend: This workshop is aimed at researchers & technical workers with a background in biology who intend to use their skills in a molecular biology lab.

Requirements

That you attend all parts of the course.

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. Experience of command-line computing and a working knowledge of R at the level of Edinburgh Genomics introductory courses.

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 online 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)