See the foot of the page for general information such as pricing and how to book.


November 23rd – 27th 2015

Course outline:

This is a five day intensive course on R and Bioconductor. The course will be a mixture of lectures and computer practicals. The final day provides participants an opportunity to analyse their own data.

No prior programming knowledge of any kind is assumed.

Course structure:

This course will be structured as follows:

  • Day 1: Introduction to R
    • Standard R data types
    • Manipulating data
    • Base graphics
  • Day 2: Bioconductor input/output
    • Object oriented programming in R
    • What is Bioconductor?
    • Installing packages
    • Loading Affymetrix and Illumina data into R
  • Day 3: Finding differentially expressed genes
    • Data quality checks
    • Microarray data analysis with Limma
  • Day 4: Functional Analysis and Data Integration
    • Clustering
    • GO stats
    • Biomart
  • Day 5: RNA-Seq and Analysis of participants’ data
    • Introduction to RNA-Seq
    • Analysis with DESeq2 and Limma Voom


  • Dr Colin Gillespie, Statistics Lecturer in the School of Mathematics & Statistics.
  • Dr Simon Cockell, Newcastle Bioinformatics Support Unit
  • John Casement, Newcastle Bioinformatics Support Unit

Book your place here.

Command Line Bioinformatics and High-throughput Sequencing Analysis

Details of the next Command Line & NGS course will be finalised in due course.

Many powerful bioinformatics applications do not come packaged with an easy-to-use graphical user interface. Since many people are unfamiliar and uncomfortable with the command-line interface that is necessary to get such applications to work, they are unable to unlock the full potential of the valuable data they are generating. The aim of this course is to enable scientists with no prior exposure to a command-line interface to get up and running with this kind of work, and provide them with the fundamentals to use any command-line application. We will start from the basics (not assuming any prior knowledge), and will move through popular bioinformatics tools such as BLAST. The second and third days of the course will focus on tools for the analysis of high-throughput (or “next generation”) sequencing data.

Course Schedule

Day 1


Linux Basics – What is Linux? What is it good for? An introduction to many basic command-line tools that we’ll build upon in the rest of the course.


BLAST – Have you ever found yourself filling in the BLAST form on the NCBI website over and over? Wondering that there must surely be a better way? There is – command-line BLAST lets you run all of those searches with a single command, and gives you far more flexibility and power than the web app ever will.

Multiple Sequence Alignments – A natural extension from the pairwise alignments of BLAST – how are all those sequences you’ve identified in your search related to one another? In this session we’ll cover tools such as ClustalW and MUSCLE.

HMMER – More powerful sequence similarity searches and domain finding with Hidden Markov Models.

Day 2


Introduction to NGS technologies, file formats such as SAM, BAM and BED, common tools such as SAMtools and BEDTools and de novo High Throughput Sequence Assembly using Velvet.


High Throughput Sequence Alignment (mapping to a reference genome) using tools such as Bowtie.

Day 3


Tools for RNA-Seq Analysis (‘Tuxedo’ pipeline: TopHat, Bowtie, Cufflinks)


RNA-Seq cont. (possibility for other analysis tools at attendees request).


Spaces can be reserved for the High Throughput Sequence Analysis course by clicking on the links in the table below, spaces on all other courses and for external people can be reserved by emailing Simon Cockell. The Bioconductor course is booked via the school of Mathematics and Statistics.  All courses are subject to a fee.

Costs for Newcastle University Faculty of Medical Sciences attendees are subsidised, except for the Bioconductor course (which is run in conjunction with the school of Mathematics and Statistics).

Booking links (Cost)
Course Length Newcastle University – FMS Newcastle University – Other External – Academic/NHS/Charity External – Commercial
Bioconductor 5 days Book (£520) Book (£520) Book (£600) Book (£800)
High Throughput
Sequence Analysis
3 days Date tba Date tba Date tba Date tba


Cancellations up to 14 days before the course start date will incur a 30 per cent cancellation fee. For later cancellations, or non attendance, the full course fee will be charged.