A Little Book of R For Bioinformatics Release 0.1 by Avril Coghlan

This is a simple introduction to bioinformatics, with a focus on genome analysis, using the R statistics software.

To encourage research into neglected tropical diseases such as leprosy, Chagas disease, trachoma, schistosomiasis etc., most of the examples in this booklet are for analysis of the genomes of the organisms that cause these diseases.

There is a pdf version of this booklet available at:

 https://github.com/avrilcoghlan/LittleBookofRBioinformatics/raw/master/_build/latex/Bioinformatics.pdf.

other booklet on using R for biomedical statistics, http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/, and my booklet on using R for time series analysis, http://a-little-book-of-r-for-time-series.readthedocs.org/.

Chapters in this Book

• How to install R and a Brief Introduction to R

• Neglected Tropical diseases

• DNA Sequence Statistics (1)

• DNA Sequence Statistics (2)

• Sequence Databases

• REVISION EXERCISES 1

• Pairwise Sequence Alignment

• Multiple Alignment and Phylogenetic trees

• REVISION EXERCISES 2

• Computational Gene-finding

• Comparative Genomics

• Hidden Markov Models

• Answers to the End-of-chapter Exercises

• Answers to Revision Exercises

• Protein-Protein Interaction Graphs

 

Acknowledgements

Noel O’Boyle for helping in using Sphinx, http://sphinx.pocoo.org, to create this document, and github, https://github.com/, to store different versions of the document and readthedocs, http://readthedocs.org/, to build and distribute this document.

Contact

(Avril Coghlan) email address [email protected]

License

The content in this book is licensed under a Creative Commons Attribution 3.0 License.

 

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