Fedora 15 Update: R-Rsolid-0.9.31-5.fc15

[updates at fedoraproject.org]

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Fedora Update Notification
FEDORA-2011-15950
2011-11-15 23:42:05
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Name        : R-Rsolid
Product     : Fedora 15
Version     : 0.9.31
Release     : 5.fc15
URL         : http://rafalab.jhsph.edu/Rsolid/
Summary     : Quantile normalization and base calling for second generation sequencing data
Description :

Rsolid is an R package for normalizing fluorescent intensity data from
ABI/SOLiD second generation sequencing platform. It has been observed
that the color-calls provided by factory software contain technical
artifacts, where the proportions of colors called are extremely
variable across sequencing cycles. Under the random DNA fragmentation
assumption, these proportions should be equal across sequencing cycles
and proportional to the dinucleotide frequencies of the sample.

Rsolid implements a version of the quantile normalization algorithm
that transforms the intensity values before calling colors. Results
show that after normalization, the total number of mappable reads
increases by around 5%, and number of perfectly mapped reads increases
by 10%. Moreover a 2-5% reduction in overall error rates is observed,
with a 2-6% reduction in the rate of valid adjacent color
mis-matches. The latter is important, since it leads to a decrease in
false-positive SNP calls.

The normalization algorithm is computationally efficient. In a test we
are able to process 300 million reads in 2 hours using 10 computer
cluster nodes. The engine functions of the package are written in C
for better performance.

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Update Information:

Update R to 2.14.0. This required a mass rebuild of R components.
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ChangeLog:

* Wed Nov  9 2011 Tom Callaway <spot at fedoraproject.org> - 0.9.31-5
- rebuild for R 2.14.0
* Thu May 19 2011 Adam Huffman <bloch at verdurin.com> - 0.9.31-4
- remove executable files to pass check
* Tue May 17 2011 Orion Poplawski <orion at cora.nwra.com> - 0.9.31-3
- Rebuild for hdf5 1.8.7
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References:

  [ 1 ] Bug #751003 - New version of R 2.14.0 is available
        https://bugzilla.redhat.com/show_bug.cgi?id=751003
  [ 2 ] Bug #753188 - Review Request: R-rtracklayer - R interface to genome browsers and their annotation tracks
        https://bugzilla.redhat.com/show_bug.cgi?id=753188
  [ 3 ] Bug #753181 - Review Request: R-RCurl - General network (HTTP/FTP) client interface for R
        https://bugzilla.redhat.com/show_bug.cgi?id=753181
  [ 4 ] Bug #753182 - Review Request: R-biomaRt - R Interface to BioMart databases
        https://bugzilla.redhat.com/show_bug.cgi?id=753182
  [ 5 ] Bug #753185 - Review Request: R-Rcompression - R Package for in-memory compression
        https://bugzilla.redhat.com/show_bug.cgi?id=753185
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This update can be installed with the "yum" update program.  Use 
su -c 'yum update R-Rsolid' at the command line.
For more information, refer to "Managing Software with yum",
available at http://docs.fedoraproject.org/yum/.

All packages are signed with the Fedora Project GPG key.  More details on the
GPG keys used by the Fedora Project can be found at
https://fedoraproject.org/keys
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