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.
|Author||Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert|
|Date of publication||None|
|Maintainer||Hans-Ulrich Klein <email@example.com>|
alignShortReads: Exact alignment of DNA sequences against a reference
AnnotatedVariants-class: Class "AnnotatedVariants"
annotateVariants: Adds genomic information to variants
assayDataAmp: Access the amplicon data of an AVASet.
ava2vcf: Convert an AVASet object into a VCF object
AVASet: Creating an AVASet
AVASet-class: Class to contain Amplicon Variant Analyzer Output
avaSetExample: Amplicon Variant Analyzer data import
avaSetFiltered: Amplicon Variant Analyzer data import
avaSetFiltered_annot: AVASet variant annotations
baseFrequency: Absolute And Relative Frequency Of The Four Bases.
baseQualityHist: Plot A Histogram Of The Base Qualities.
baseQualityStats: Statistics Of Base Quality
breakpoints: Putative breakpoints of chimeric reads
Breakpoints-class: Class "Breakpoints"
calculateTiTv: Calculate transition transversion ratio
captureArray: Custom capture array design
complexity.dust: Sequence Complexity Using The DUST Algorithm
complexity.entropy: Sequence Complexity Using The Shannon-Wiener Algorithm
convertCigar: Basic functions for CIGAR strings
coverageOnTarget: Computes the coverage restricted to the target region.
demultiplexReads: Performs MID/Multiplex filtering
detectBreakpoints: Clustering and consensus breakpoint detection for chimeric...
dinucleotideOddsRatio: Dinucleotide Odds Ratio
fDataAmp: Access the amplicon data of an AVASet.
featureDataAmp: Access the amplicon data of an AVASet
filterChimericReads: Extract chimeric reads and apply filtering steps to remove...
flowgramBarplot: Create A Barplot Of The Flow Intensities
gcContent: Calculate The Overall GC-Content
gcContentHist: GC-Content Histogram
gcPerPosition: GC-Content Per Position
genomeSequencerMIDs: Retrieve GS multiplex sequences
getAlignedReads: Import reads from an Amplicon Variant Analyzer project
getAminoAbbr: Get amino acid abbreviations
getVariantPercentages: Variant coverage
homopolymerHist: Create A Histogram Of The Homopolymer Stretches
htmlReport: HTML-Report Builder for the AVASet and MapperSet
MapperSet: Creating a MapperSet
MapperSet-class: Class to Contain GS Reference Mapper Output
mapperSetExample: GS Reference Mapper data import
mergeBreakpoints: Identify and merge related breakpoints caused by the same...
mutationInfo: Example data for 'plotVariants'
nucleotideCharts: Nucleotide Charts
plotAmpliconCoverage: Creates a plot visualizing the number of reads per amplicon
plotChimericReads: Plots chimeric reads
plotVariants: Plots variant positions
plotVariationFrequency: Create an AVA style variation frequency plot
positionQualityBoxplot: Boxplot Of The Quality For Each Position
qualityReportSFF: Function To Create A Quality Report In PDF Format
readLengthHist: Histogram Of The Read Lengths
readLengthStats: Statistics For The Read Lengths
readSFF: Function To Read In Roche's .sff Files
readsOnTarget: Check for each read whether it aligns within the given...
referenceSequences: Access the reference sequences of an AVASet
regions: Example data for 'plotVariants'
removeLinker: Remove linker sequences located at the start of short reads
sequenceCaptureLinkers: Retrieve NimbleGen's sequence capture linkers
sequenceQualityHist: A Histogram Of The Sequence Qualities
setVariantFilter: Filters output of variant information
sff2fastq: Write A SFFContainer Object To A FASTQ File
SFFContainer-class: Class '"SFFContainer"'
SFFRead-class: Class '"SFFRead"'
variants: Example data for 'plotVariants'
writeSFF: Function To Write Files In Roche's .sff Format