R-Rsolid-0.9.31-alt1_29.i586.rpm


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Description

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

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports i586
Package filename R-Rsolid-0.9.31-alt1_29.i586.rpm
Package name R-Rsolid
Package version 0.9.31
Package release alt1_29
Package architecture i586
Package type rpm
Category Other
Homepage -
License -
Maintainer -
Download size 51.65 KB
Installed size 51.65 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.

Alternatives

Package Version Architecture Repository
R-Rsolid-0.9.31-alt1_29.x86_64.rpm 0.9.31 x86_64 Autoimports
R-Rsolid - - -

Requires

Name Value
libR.so -
libc.so.6(GLIBC_2.0) -
libc.so.6(GLIBC_2.1.3) -
libc.so.6(GLIBC_2.3.4) -
libc.so.6(GLIBC_2.4) -
libhdf5.so.8 -
rpmlib(PayloadIsLzma) -
rpmlib(SetVersions) -
rtld(GNU_HASH) -

Provides

Name Value
R-Rsolid = 0.9.31-alt1_29

Download

Type URL
Mirror ftp.altlinux.org
Binary Package R-Rsolid-0.9.31-alt1_29.i586.rpm
Source Package R-Rsolid-0.9.31-alt1_29.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus i586 autoimports
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    
  2. Update the package index:
    # sudo apt-get update
  3. Install R-Rsolid rpm package:
    # sudo apt-get install R-Rsolid

Files

Path
/usr/lib/R/library/Rsolid/DESCRIPTION
/usr/lib/R/library/Rsolid/INDEX
/usr/lib/R/library/Rsolid/NAMESPACE
/usr/lib/R/library/Rsolid/Meta/Rd.rds
/usr/lib/R/library/Rsolid/Meta/data.rds
/usr/lib/R/library/Rsolid/Meta/features.rds
/usr/lib/R/library/Rsolid/Meta/hsearch.rds
/usr/lib/R/library/Rsolid/Meta/links.rds
/usr/lib/R/library/Rsolid/Meta/nsInfo.rds
/usr/lib/R/library/Rsolid/Meta/package.rds
/usr/lib/R/library/Rsolid/R/Rsolid
/usr/lib/R/library/Rsolid/R/Rsolid.rdb
/usr/lib/R/library/Rsolid/R/Rsolid.rdx
/usr/lib/R/library/Rsolid/data/prop.Hs.rda
/usr/lib/R/library/Rsolid/help/AnIndex
/usr/lib/R/library/Rsolid/help/Rsolid.rdb
/usr/lib/R/library/Rsolid/help/Rsolid.rdx
/usr/lib/R/library/Rsolid/help/aliases.rds
/usr/lib/R/library/Rsolid/help/paths.rds
/usr/lib/R/library/Rsolid/html/00Index.html
/usr/lib/R/library/Rsolid/html/Rsolid.html
/usr/lib/R/library/Rsolid/libs/Rsolid.so

See Also

Package Description
R-Rsolid-devel-0.9.31-alt1_29.i586.rpm Development files for R-Rsolid
R-affyio-1.50.0-alt1_5.i586.rpm Tools for parsing Affymetrix data files
R-argon2-0.2.0-alt1_7.i586.rpm Secure Password Hashing
R-backports-1.1.4-alt1_3.i586.rpm Reimplementations of Functions Introduced Since R-3.0.0
R-base64enc-0.1.3-alt1_6.i586.rpm Tools for base64 encoding
R-bit-1.1.14-alt1_4.i586.rpm A class for vectors of 1-bit booleans
R-bit64-0.9.7-alt1_7.i586.rpm A S3 Class for Vectors of 64bit Integers
R-bitops-1.0.6-alt1_13.i586.rpm Functions for Bitwise operations
R-caTools-1.17.1.2-alt1_1.i586.rpm Tools: moving window statistics, GIF, Base64, ROC AUC, etc
R-chron-2.3.54-alt1_1.i586.rpm Chronological Objects which can Handle Dates and Times
R-colorspace-1.4.1-alt1_3.i586.rpm A Toolbox for Manipulating and Assessing Colors and Palettes
R-cran-Cairo-1.5.9-alt1_2.i586.rpm A cairo bindings for R
R-date-1.2.38-alt1_6.i586.rpm Functions for Handling Dates
R-digest-0.6.15-alt1_6.i586.rpm Create Cryptographic Hash Digest of R Objects
R-digest-devel-0.6.15-alt1_6.i586.rpm Header files for compiling against digest
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