Dear all, please could you recommend any R package where the interchromosomal interactions (by 3C method - chromatin conformation capture) could be visualized? thanks, Bogdan [[alternative HTML version deleted]]

Hi Bogdan, There is a package called r3Cseq, could be used for visualization. please see examples in its vignette. There is also a package called ggbio, for general visualization of sequencing data, in the vignette, a function called plotOverview plot information(GRanges) as segment or rectangle on a stacked genome. which layout all chromosomes one by one, and you could arrange your interaction as a GRanges object, then adding them on the plot as the example shows. FYI: this part will be generalized into a layout_stacked() in the next release. If you have any question about it, feel free to sent me email anytime. thanks. HTH Tengfei On Wed, Jan 25, 2012 at 10:15 AM, Bogdan Tanasa <tanasa@gmail.com> wrote: > Dear all, > > please could you recommend any R package where the > interchromosomal interactions (by 3C method - chromatin conformation > capture) could be visualized? > > thanks, > > Bogdan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]

Bogdan Tanasa scripsit 01/25/2012 05:15 PM: > Dear all, > > please could you recommend any R package where the > interchromosomal interactions (by 3C method - chromatin conformation > capture) could be visualized? > > thanks, > > Bogdan Some simple visualisations of inter-chromosomal interaction patterns and associated example code are also in the vignette of the LiebermanAidenHiC2009 data package: http://www.bioconductor.org/packages/release/data/experiment/html/Lieb ermanAidenHiC2009.html Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber