Last data update: 2014.03.03
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R453Plus1Toolbox
Package: R453Plus1Toolbox
Type: Package
Title: A package for importing and analyzing data from Roche's Genome
Sequencer System
Version: 1.22.0
Date: 2016-01-11
Author: Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert
Maintainer: Hans-Ulrich Klein <h.klein@uni-muenster.de>
Depends: R (>= 2.12.0), methods, VariantAnnotation, Biostrings, Biobase
Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML,
TeachingDemos, BiocGenerics, S4Vectors (>= 0.9.25), IRanges,
XVector, GenomicRanges, SummarizedExperiment, biomaRt,
BSgenome, Rsamtools, ShortRead
Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Scerevisiae.UCSC.sacCer2
Description: The R453Plus1 Toolbox comprises useful functions for the
analysis of data generated by Roche's 454 sequencing platform.
It adds functions for quality assurance as well as for
annotation and visualization of detected variants,
complementing the software tools shipped by Roche with their
product. Further, a pipeline for the detection of structural
variants is provided.
License: LGPL-3
biocViews: Sequencing, Infrastructure, DataImport, DataRepresentation,
Visualization, QualityControl, ReportWriting
NeedsCompilation: yes
Packaged: 2016-05-05 02:38:49 UTC; biocbuild
● BiocViews: DataImport, DataRepresentation, Infrastructure, QualityControl, ReportWriting, Sequencing, Visualization
●
2 images,
55 functions,
9 datasets
●
Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'R453Plus1Toolbox' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c readSFF.c -o readSFF.o
readSFF.c: In function 'readSFF':
readSFF.c:46:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, fileLen, 1, file);
^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c writeSFF.c -o writeSFF.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o R453Plus1Toolbox.so readSFF.o writeSFF.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/R453Plus1Toolbox/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'R453Plus1Toolbox'
finding HTML links ... done
AVASet-class html
finding level-2 HTML links ... done
AVASet html
AnnotatedVariants-class html
Breakpoints-class html
MapperSet-class html
MapperSet html
SFFContainer-class html
SFFRead-class html
alignShortReads html
annotateVariants html
assayDataAmp html
ava2vcf html
avaSetExample html
avaSetFiltered html
avaSetFiltered_annot html
baseFrequency html
baseQualityHist html
baseQualityStats html
breakpoints html
calculateTiTv html
captureArray html
complexity.dust html
complexity.entropy html
convertCigar html
coverageOnTarget html
demultiplexReads html
detectBreakpoints html
dinucleotideOddsRatio html
fDataAmp html
featureDataAmp html
filterChimericReads html
flowgramBarplot html
gcContent html
gcContentHist html
gcPerPosition html
genomeSequencerMIDs html
getAlignedReads html
getAminoAbbr html
getVariantPercentages html
homopolymerHist html
htmlReport html
mapperSetExample html
mergeBreakpoints html
mutationInfo html
nucleotideCharts html
plotAmpliconCoverage html
plotChimericReads html
plotVariants html
plotVariationFrequency html
positionQualityBoxplot html
qualityReportSFF html
readLengthHist html
readLengthStats html
readSFF html
readsOnTarget html
referenceSequences html
regions html
removeLinker html
sequenceCaptureLinkers html
sequenceQualityHist html
setVariantFilter html
sff2fastq html
variants html
writeSFF html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (R453Plus1Toolbox)
Making 'packages.html' ... done
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