New Bioconductor package: rtracklayer
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This is a formal announcement of rtracklayer, a new package in Bioconductor 2.2. The rtracklayer package links R/Bioconductor to existing genome browsers. The package defines a common interface through which the R user may control any genome browser for which a driver exists. The two primary capabilities of the rtracklayer interface are: (1) transferring annotation tracks to and from genome browsers and (2) creating, manipulating and querying the state of browser views. Currently, there are built-in drivers for the UCSC and Argo browsers and soon for the GenomeGraphs Bioconductor package; support may be added for any other browser by loading the appropriate driver (if one exists) into the R session. The package also defines the trackSet class, which extends the base Bioconductor data structure, eSet, to enable the storage of annotation tracks within the Bioconductor framework. There is a vignette in the package that demonstrates a simple session. We are very interested in any feedback, especially any suggestions about how rtracklayer could be improved to best support your work. Our goal is the seamless integration of rtracklayer with analysis of experimental data from any source: expression arrays, tiling arrays, CGH data, SNPs, high-throughput sequencing data, etc. If you are familiar with the analysis of one or more of these data types, please tell us how rtracklayer can serve you better. Thank you, Michael Lawrence [[alternative HTML version deleted]]
Sequencing Annotation CGH GenomeGraphs rtracklayer Sequencing Annotation CGH GenomeGraphs • 633 views

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