seqTools-package: SeqTools: Bioconductor package for analysis of FASTQ and...
In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.
Description
Details
Author(s)
References
Examples
Description
Analyze read length, phred scores and alphabeth frequency
and DNA k-mers on uncompressed and compressed files.
Details
Package: seqTools
Type: Package
Version: 0.99.31
Date: 2013-10-14
License: GPL-2
Depends: methods
Author(s)
Wolfgang Kaisers
Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
References
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM
The sanger FASTQ file format for sequences with quality scores and
the Solexa/Illumina FASTQ variants.
Nucleic Acids Research 2010 Vol.38 No.6 1767-1771
Examples
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# A) Count DNA k-mer
countDnaKmers("ATAAATA", 2)
# B) Quality check on FASTQ file
basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
fq <- fastqq("test_l6.fq")
plotPhredQuant(fq, 1)
wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.
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Description Details Author(s) References Examples
Description
Analyze read length, phred scores and alphabeth frequency and DNA k-mers on uncompressed and compressed files.
Details
| Package: | seqTools |
| Type: | Package |
| Version: | 0.99.31 |
| Date: | 2013-10-14 |
| License: | GPL-2 |
| Depends: | methods |
Author(s)
Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
References
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-1771
Examples
1 2 3 4 5 6 7 | # A) Count DNA k-mer
countDnaKmers("ATAAATA", 2)
# B) Quality check on FASTQ file
basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
fq <- fastqq("test_l6.fq")
plotPhredQuant(fq, 1)
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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