[BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Thu Nov 10 20:13:06 CET 2011


Here is a presentation by Xuekui Zhang,Eloi Mercier and Arnaud Droit on
analyzing ChIP-seq dataset using Bioconductor packages at the Bioc2011
Seattle meeting. 

Hope this is what you are looking for.

Best regards,


On 11/10/11 1:47 PM, "Julie Zhu" <julie.zhu at umassmed.edu> wrote:

> Halian,
> For functionalities of ChIPpeakAnno, please refer to
> http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/ChI
> PpeakAnno-BioC2011.pdf and
> Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS and Green MR.
> (2010)  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and
> ChIP-chip data. BMC Bioinformatics 2010, 11:237 which also gives an overview
> of Bioconductor packages for ChIP-seq data analysis
> There are several peak calling algorithms available in Bioconductor
> http://bioconductor.org/packages/release/bioc/. In addition, there are other
> peak calling algorithms outside of Bioconductor
> Evaluation of Algorithm Performance in ChIP-Seq Peak Detection (Elizabeth et
> al., 2010.PLoS one 5(7):e11471)
> Laajala et al., 2009 A practical comparison of methods for detecting
> transcription factor binding sites in ChIP-seq experiments. BMC
> Bioinformatics 10:618 doi:10.1186/1471-2164-10-618
> Best regards,
> Julie
> On 11/10/11 12:56 PM, "Halian Vilela" <halianlian at gmail.com> wrote:
>> Julie, thanks for the fast answer.
>> Yes, I was using the reads directly. Surely I misunderstood the kind of data
>> the function should work with.
>> What peak calling algorithm should I use then ? Are there any function to do
>> this in your package ? If not, could you suggest me any (package) ?
>> Thanks a lot.
>> Halian

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