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Michael Lawrence
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620
@michael-lawrence-2759
Last seen 10.3 years ago
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
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