R-Rsolid - Quantile normalization and base calling for second generation sequencing data

Property Value
Distribution Fedora 28
Repository Fedora i386
Package filename R-Rsolid-0.9.31-22.fc27.i686.rpm
Package name R-Rsolid
Package version 0.9.31
Package release 22.fc27
Package architecture i686
Package type rpm
Category Applications/Engineering
Homepage http://rafalab.jhsph.edu/Rsolid/
License Artistic 2.0
Maintainer -
Download size 38.21 KB
Installed size 43.84 KB
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.


Package Version Architecture Repository
R-Rsolid-0.9.31-24.fc28.i686.rpm 0.9.31 i686 Fedora Updates
R-Rsolid-0.9.31-24.fc28.i686.rpm 0.9.31 i686 Fedora Updates
R-Rsolid-0.9.31-24.fc28.x86_64.rpm 0.9.31 x86_64 Fedora Updates
R-Rsolid-0.9.31-22.fc27.i686.rpm 0.9.31 i686 Fedora
R-Rsolid-0.9.31-22.fc27.x86_64.rpm 0.9.31 x86_64 Fedora
R-Rsolid - - -


Name Value
R-core >= 3.4.0
libR.so -
libc.so.6(GLIBC_2.4) -
libhdf5.so.10 -
rtld(GNU_HASH) -


Name Value
R-Rsolid = 0.9.31-22.fc27
R-Rsolid(x86-32) = 0.9.31-22.fc27


Type URL
Mirror download-ib01.fedoraproject.org
Binary Package R-Rsolid-0.9.31-22.fc27.i686.rpm
Source Package R-Rsolid-0.9.31-22.fc27.src.rpm

Install Howto

Install R-Rsolid rpm package:

# dnf install R-Rsolid




2017-08-02 - Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-22
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
2017-07-26 - Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-21
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
2017-05-31 - Tom Callaway <spot@fedoraproject.org> - 0.9.31-20
- rebuild for R 3.4.0
2017-02-10 - Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-19
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
2016-02-03 - Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-18
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
2016-01-21 - Orion Poplawski <orion@cora.nwra.com> - 0.9.31-17
- Rebuild for hdf5 1.8.16
2015-06-16 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-16
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
2015-05-17 - Orion Poplawski <orion@cora.nwra.com> - 0.9.31-15
- Rebuild for hdf5 1.8.15
2015-01-07 - Orion Poplawski <orion@cora.nwra.com> - 0.9.31-14
- Rebuild for hdf5 1.8.14
2014-08-15 - Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-13
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild

See Also

Package Description
R-Rsolid-devel-0.9.31-22.fc27.i686.rpm Development files for R-Rsolid
R-S4Vectors-0.16.0-1.fc28.i686.rpm S4 implementation of vectors and lists
R-S4Vectors-devel-0.16.0-1.fc28.i686.rpm Development files for R-S4Vectors
R-SEDML-0.4.3-8.fc28.i686.rpm R library that fully supports SED-ML for SBML
R-SummarizedExperiment-1.8.1-1.fc28.noarch.rpm SummarizedExperiment container
R-TH-data-1.0.3-3.fc23.noarch.rpm Data for other R packages
R-V8-1.5-4.fc28.i686.rpm Embedded JavaScript Engine for R
R-XML- Tools for parsing and generating xml within r and s-plus
R-XVector-0.18.0-1.fc28.i686.rpm Representation and manipulation of external sequences
R-XVector-devel-0.18.0-1.fc28.i686.rpm Development files for R-XVector
R-abind-1.4.5-1.fc28.noarch.rpm Combine multi-dimensional arrays
R-acepack-1.4.1-6.fc28.i686.rpm ACE and AVAS methods for choosing regression transformations
R-affy-1.54.0-3.fc27.i686.rpm Methods for Affymetrix Oligonucleotide Arrays
R-affydata-1.16.0-2.fc24.noarch.rpm Affymetrix data for demonstration purpose
R-affyio-1.46.0-3.fc27.i686.rpm Tools for parsing Affymetrix data files