ChIP Course

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NuGO DNA methylation microarray course (Newcastle 2010)

General information

The course centers on the analysis of data arising from ChIP-on-chip and DNA methylation technology and is aimed at any PhD student or Post-doc interested in getting a feeling for the underlying bioinformatics work flow. The course describes a complete analysis pipeline, starting at raw data (ones and zeros) and ending at the biological interpretation of this data through pathway and sequence analysis. It is a two-day course involving both lectures and hands-on sessions. During these hands-on sessions, a carefully selected example dataset is used.

Day 1 will focus on ChIP and DNA methylation array technology and raw data processing. Day 2 will focus on combining multiple bioinformatics approaches and additional data to maximize the biological interpretation of the processed data. After the course, you will be able to analyze ChIP and DNA methylation data on a basic level from start (raw data) to finish (biological interpretation).


Please contact one of the course organizers if you would like handouts of the presentations.


Using the NX client to login to the R server

NX R server

Some basic R commands

Basic R

Day 1

Raw data processing

Day 2

Sequence analysis

Pathway Analysis

Further reading

If you want to learn a little bit more R, the following books are recommended (especially the first one):

The following web-pages contain many useful examples and tutorials:

Using Google to find information on R (or one of its packages) often yields no useful results. Use this custom search instead:

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