I have been spending more and more time learning R because a lot of the statistical procedures used in bioinformatics are being made available (most times exclusively) via R and Bioconductor. As I keep learning more about R, I am continually impressed with its capabilities and wondered why I did not learn it earlier. Do not make the same mistake, learn R as soon as possible if you are serious about data analysis!

For those coming from a biological background (like myself) and want to learn R with respect to data analysis and visualisation of high throughput sequencing data, have a look at the material provided by the UC Davis Bioinformatics Core.

The Bioinformatics Data Skills book also has a nice chapter on getting started with R (among other bioinformatic topics).

You can click on the R tag, to retrieve most of my posts related to R. I say most because I am sure I have forgotten to add the R tag to a few posts. Lastly, as with the rest of my site, I use this site as a learning tool for myself so please view everything with a grain of salt (and please let me know where I have erred!).


Must read

There are some must read articles available at the R Manuals page, such as An Introduction to R and R Data Import/Export.

Links to R resources

Useful R packages

Bioconductor packages

  • ctc
  • edgeR
  • DESeq
  • baySeq
  • GO.db
  • GOstats
  • biomaRt
  • Ringo
  • ShortRead
  • org.Hs.eg.db
  • goseq
  • Rsamtools
  • GenomicRanges
  • IRanges
  • CAGEr

CRAN packages

  • gplots
  • ggplot2
  • tm
  • seqinr
  • data.table
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6 comments Add yours
    1. Hi Siewfong,

      Glad it helped! A PCA is not the easiest thing to grasp; sometimes I have to look back at the post to remind myself.



      1. Now the challenge is to understand my results, and explain that. Will try to have fun there…… 🙂

        Have a good day and keep up the (generous) good work!

  1. 100 percent agree with you !
    R is pretty suitable for us who are biological background like you and me, help us to avoid taking a roundabout course both in our study and work .
    however, It’s really not easy for most of us to learn it well by ourselves, we should keep practice and communicate with each other.
    I am lucky to see you blog, Thank you again .

    Call me Jimmy

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