[BioC] tutorials for RNA-seq analysis in Bioconductor

[Hans-Rudolf Hotz]

On 05/22/2013 10:53 PM, Steve Lianoglou wrote:
> Hi,
>
> On Wed, May 22, 2013 at 1:36 PM, Fiona Ingleby <fiona.ingleby at gmail.com> wrote:
>> Hi everyone,
>>
>> Quick question: can anyone recommend tutorials/resources which are available online that I could use to get started with the basics of analysing RNA-seq data in Bioconductor? I've come across a few things (sets of lecture slides and sets of code to work through) but I just thought I would ask if anyone had found anything particularly useful? Ideally I'm wanting to focus on alignment and differential expression analysis, so I'd be grateful if anyone has any recommendations.
>
> Reading through the vignettes for packages built to handle these
> things would be a good start, namely:
>
> * easyRNASeq
>    http://bioconductor.org/packages/2.12/bioc/vignettes/easyRNASeq/inst/doc/easyRNASeq.pdf
>
> * HTSeqGene
>    http://bioconductor.org/packages/2.12/bioc/vignettes/HTSeqGenie/inst/doc/HTSeqGenie.pdf
>
> * QuasR
>    http://bioconductor.org/packages/2.12/bioc/vignettes/QuasR/inst/doc/QuasR-Overview.pdf
>
>
> HTH,
> -steve
>

and check out the 'Sample Workflow' on the Bioconductor home page:

http://www.bioconductor.org/help/workflows/high-throughput-sequencing/


also, the IIGB at UCRiverside has an excellent collection of manuals, eg:
http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-RNA-Seq-Analysis


Regards, Hans-Rudolf


> --
> Steve Lianoglou
> Computational Biologist
> Department of Bioinformatics and Computational Biology
> Genentech
>
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