Package: R453Plus1Toolbox 1.57.0
Hans-Ulrich Klein
R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System
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.
Authors:
R453Plus1Toolbox_1.57.0.tar.gz
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R453Plus1Toolbox.pdf |R453Plus1Toolbox.html✨
R453Plus1Toolbox/json (API)
NEWS
| # Install 'R453Plus1Toolbox' in R: |
| install.packages('R453Plus1Toolbox', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- avaSetExample - Amplicon Variant Analyzer data import
- avaSetFiltered - Amplicon Variant Analyzer data import
- avaSetFiltered_annot - AVASet variant annotations
- breakpoints - Putative breakpoints of chimeric reads
- captureArray - Custom capture array design
- mapperSetExample - GS Reference Mapper data import
- mutationInfo - Example data for 'plotVariants'
- regions - Example data for 'plotVariants'
- variants - Example data for 'plotVariants'
On BioConductor:R453Plus1Toolbox-1.57.0(bioc 3.21)R453Plus1Toolbox-1.56.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencinginfrastructuredataimportdatarepresentationvisualizationqualitycontrolreportwriting
Last updated 2 months agofrom:8d481bd431. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 01 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 01 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 01 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 01 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 01 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 01 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 01 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 01 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 01 2024 |
Exports:addReadalignedReadsC1alignedReadsC1<-alignedReadsC2alignedReadsC2<-alignShortReadsannotatedVariantsannotateVariantsassayDataAmpassayDataAmp<-ava2vcfAVASetbaseFrequencybaseQualityHistbaseQualityStatscalculateTiTvclipAdapterLeftclipAdapterLeft<-clipAdapterRightclipAdapterRight<-clipQualityLeftclipQualityLeft<-clipQualityRightclipQualityRight<-commonAlignC1commonAlignC1<-commonAlignC2commonAlignC2<-commonBpsC1commonBpsC1<-commonBpsC2commonBpsC2<-complexity.dustcomplexity.entropycoverageOnTargetdemultiplexReadsdetectBreakpointsdinucleotideOddsRatioextendedCIGARToListfDataAmpfeatureDataAmpfeatureDataAmp<-filterChimericReadsflowCharsflowChars<-flowgramflowgram<-flowgramBarplotflowgramFormatflowgramFormat<-flowgramsflowgrams<-flowIndexesflowIndexes<-gcContentgcContentHistgcPerPositiongenomeSequencerMIDsgetAlignedReadsgetReadgetReadStatusgetVariantPercentageshomopolymerHisthtmlReportkeySequencekeySequence<-listToExtendedCIGARMapperSetmergeBreakpointsnamename<-nucleotideChartsplotAmpliconCoverageplotChimericReadsplotVariantsplotVariationFrequencypositionQualityBoxplotqualityquality<-qualityReportSFFreadread<-readLengthHistreadLengthStatsreadsreads<-readSFFreadsOnTargetreferenceSequencesreferenceSequences<-removeLinkerseqsC1seqsC1<-seqsC2seqsC2<-sequenceCaptureLinkerssequenceQualityHistsetVariantFiltersff2fastqwriteSFF
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydeldirdigestdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2hwriterinterpIRangesjpegjsonliteKEGGRESTlambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrpwalignR2HTMLR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsShortReadsnowSparseArraystringistringrSummarizedExperimentsysTeachingDemostibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Exact alignment of DNA sequences against a reference | alignShortReads alignShortReads,AVASet,BSgenome,character,logical-method alignShortReads,AVASet,BSgenome,character,missing-method alignShortReads,AVASet,BSgenome,missing,logical-method alignShortReads,AVASet,BSgenome,missing,missing-method alignShortReads,DNAStringSet,BSgenome,character,logical-method alignShortReads,DNAStringSet,BSgenome,character,missing-method alignShortReads,DNAStringSet,BSgenome,missing,logical-method alignShortReads,DNAStringSet,BSgenome,missing,missing-method |
| Class "AnnotatedVariants" | annotatedVariants annotatedVariants,AnnotatedVariants-method AnnotatedVariants-class annotatedVariants<-,AnnotatedVariants,list-method names,AnnotatedVariants-method names<-,AnnotatedVariants,character-method |
| Adds genomic information to variants | annotateVariants annotateVariants,AVASet,missing-method annotateVariants,data.frame,missing-method annotateVariants,MapperSet,BSgenome-method annotateVariants,MapperSet,missing-method |
| Access the amplicon data of an AVASet. | assayDataAmp |
| Convert an AVASet object into a VCF object | ava2vcf ava2vcf,AVASet-method |
| Creating an AVASet | AVASet AVASet,character,character,missing,missing,missing,missing,missing-method AVASet,character,missing,character,character,character,character,character-method AVASet,character,missing,character,character,character,missing,missing-method AVASet,character,missing,missing,missing,missing,missing,missing-method |
| Class to contain Amplicon Variant Analyzer Output | alignShortReads,AVASet,DNAStringSet,character-method annotateVariants,AVASet-method assayDataAmp,AVASet-method assayDataAmp<- assayDataAmp<-,AVASet,AssayData-method AVASet-class fDataAmp,AVASet-method featureDataAmp,AVASet-method featureDataAmp<- featureDataAmp<-,AVASet,AnnotatedDataFrame-method getVariantPercentages,AVASet-method htmlReport,AVASet-method referenceSequences,AVASet-method referenceSequences<- referenceSequences<-,AVASet,AlignedRead-method setVariantFilter,AVASet-method [,AVASet,ANY,ANY,ANY-method [,AVASet,ANY,ANY-method |
| Amplicon Variant Analyzer data import | avaSetExample |
| Amplicon Variant Analyzer data import | avaSetFiltered |
| AVASet variant annotations | avaSetFiltered_annot |
| Absolute And Relative Frequency Of The Four Bases. | baseFrequency baseFrequency,DNAStringSet-method baseFrequency,SFFContainer-method baseFrequency,ShortRead-method |
| Plot A Histogram Of The Base Qualities. | baseQualityHist baseQualityHist,QualityScaledDNAStringSet-method baseQualityHist,SFFContainer-method baseQualityHist,ShortReadQ-method |
| Statistics Of Base Quality | baseQualityStats baseQualityStats,QualityScaledDNAStringSet-method baseQualityStats,SFFContainer-method baseQualityStats,ShortReadQ-method |
| Putative breakpoints of chimeric reads | breakpoints |
| Class "Breakpoints" | alignedReadsC1 alignedReadsC1,Breakpoints-method alignedReadsC1<- alignedReadsC1<-,Breakpoints,list-method alignedReadsC2 alignedReadsC2,Breakpoints-method alignedReadsC2<- alignedReadsC2<-,Breakpoints,list-method Breakpoints-class commonAlignC1 commonAlignC1,Breakpoints-method commonAlignC1<- commonAlignC1<-,Breakpoints,list-method commonAlignC2 commonAlignC2,Breakpoints-method commonAlignC2<- commonAlignC2<-,Breakpoints,list-method commonBpsC1 commonBpsC1,Breakpoints-method commonBpsC1<- commonBpsC1<-,Breakpoints,list-method commonBpsC2 commonBpsC2,Breakpoints-method commonBpsC2<- commonBpsC2<-,Breakpoints,list-method length,Breakpoints-method mergeBreakpoints,Breakpoints,missing,list-method mergeBreakpoints,Breakpoints,missing,missing-method mergeBreakpoints,Breakpoints,numeric,missing-method names,Breakpoints-method names<-,Breakpoints,ANY-method plotChimericReads,Breakpoints-method seqsC1 seqsC1,Breakpoints-method seqsC1<- seqsC1<-,Breakpoints,list-method seqsC2 seqsC2,Breakpoints-method seqsC2<- seqsC2<-,Breakpoints,list-method [,Breakpoints,ANY,ANY,ANY-method [,Breakpoints,ANY,ANY-method |
| Calculate transition transversion ratio | calculateTiTv calculateTiTv,AVASet-method calculateTiTv,MapperSet-method |
| Custom capture array design | captureArray |
| Sequence Complexity Using The DUST Algorithm | complexity.dust complexity.dust,DNAStringSet-method complexity.dust,SFFContainer-method complexity.dust,ShortRead-method |
| Sequence Complexity Using The Shannon-Wiener Algorithm | complexity.entropy complexity.entropy,DNAStringSet-method complexity.entropy,SFFContainer-method complexity.entropy,ShortRead-method |
| Basic functions for CIGAR strings | convertCigar extendedCIGARToList listToExtendedCIGAR |
| Computes the coverage restricted to the target region. | coverageOnTarget coverageOnTarget,list,GRanges-method |
| Performs MID/Multiplex filtering | demultiplexReads demultiplexReads,XStringSet,XStringSet,missing,logical-method demultiplexReads,XStringSet,XStringSet,missing,missing-method demultiplexReads,XStringSet,XStringSet,numeric,logical-method demultiplexReads,XStringSet,XStringSet,numeric,missing-method |
| Clustering and consensus breakpoint detection for chimeric reads | detectBreakpoints detectBreakpoints,list-method |
| Dinucleotide Odds Ratio | dinucleotideOddsRatio dinucleotideOddsRatio,DNAStringSet-method dinucleotideOddsRatio,SFFContainer-method dinucleotideOddsRatio,ShortRead-method |
| Access the amplicon data of an AVASet. | fDataAmp |
| Access the amplicon data of an AVASet | featureDataAmp |
| Extract chimeric reads and apply filtering steps to remove artificial chimeric reads. | filterChimericReads filterChimericReads,list,IntegerRangesList,DNAString,missing,missing-method filterChimericReads,list,IntegerRangesList,DNAString,numeric,numeric-method filterChimericReads,list,IntegerRangesList,missing,missing,missing-method filterChimericReads,list,IntegerRangesList,missing,numeric,numeric-method filterChimericReads,list,missing,DNAString,missing,missing-method filterChimericReads,list,missing,DNAString,numeric,numeric-method filterChimericReads,list,missing,missing,missing,missing-method filterChimericReads,list,missing,missing,numeric,numeric-method |
| Create A Barplot Of The Flow Intensities | flowgramBarplot flowgramBarplot,SFFRead-method |
| Calculate The Overall GC-Content | gcContent gcContent,DNAStringSet-method gcContent,SFFContainer-method gcContent,ShortRead-method |
| GC-Content Histogram | gcContentHist gcContentHist,DNAStringSet-method gcContentHist,SFFContainer-method gcContentHist,ShortRead-method |
| GC-Content Per Position | gcPerPosition gcPerPosition,DNAStringSet-method gcPerPosition,SFFContainer-method gcPerPosition,ShortRead-method |
| Retrieve GS multiplex sequences | genomeSequencerMIDs genomeSequencerMIDs,character-method genomeSequencerMIDs,missing-method |
| Import reads from an Amplicon Variant Analyzer project | getAlignedReads getAlignedReads,AVASet-method |
| Get amino acid abbreviations | getAminoAbbr |
| Variant coverage | getVariantPercentages |
| Create A Histogram Of The Homopolymer Stretches | homopolymerHist homopolymerHist,SFFRead-method |
| HTML-Report Builder for the AVASet and MapperSet | htmlReport |
| Creating a MapperSet | MapperSet MapperSet,character-method |
| Class to Contain GS Reference Mapper Output | annotateVariants,MapperSet-method getReadStatus getReadStatus,MapperSet-method getVariantPercentages,MapperSet-method htmlReport,MapperSet-method MapperSet-class setVariantFilter,MapperSet-method |
| GS Reference Mapper data import | mapperSetExample |
| Identify and merge related breakpoints caused by the same variant. | mergeBreakpoints |
| Example data for 'plotVariants' | mutationInfo |
| Nucleotide Charts | nucleotideCharts nucleotideCharts,DNAStringSet-method nucleotideCharts,SFFContainer-method nucleotideCharts,ShortRead-method |
| Creates a plot visualizing the number of reads per amplicon | plotAmpliconCoverage plotAmpliconCoverage,AVASet,character,logical-method plotAmpliconCoverage,AVASet,character,missing-method plotAmpliconCoverage,AVASet,missing,logical-method plotAmpliconCoverage,AVASet,missing,missing-method |
| Plots chimeric reads | plotChimericReads |
| Plots variant positions | plotVariants plotVariants,AnnotatedVariants,character-method plotVariants,data.frame,character-method |
| Create an AVA style variation frequency plot | plotVariationFrequency plotVariationFrequency,character,numeric-method |
| Boxplot Of The Quality For Each Position | positionQualityBoxplot positionQualityBoxplot,QualityScaledDNAStringSet-method positionQualityBoxplot,SFFContainer-method positionQualityBoxplot,ShortReadQ-method |
| Function To Create A Quality Report In PDF Format | qualityReportSFF |
| Histogram Of The Read Lengths | readLengthHist readLengthHist,DNAStringSet-method readLengthHist,SFFContainer-method readLengthHist,ShortRead-method |
| Statistics For The Read Lengths | readLengthStats readLengthStats,DNAStringSet-method readLengthStats,SFFContainer-method readLengthStats,ShortRead-method |
| Function To Read In Roche's .sff Files | readSFF |
| Check for each read whether it aligns within the given region. | readsOnTarget readsOnTarget,list,GRanges-method |
| Access the reference sequences of an AVASet | referenceSequences |
| Example data for 'plotVariants' | regions |
| Remove linker sequences located at the start of short reads | removeLinker removeLinker,XStringSet,DNAString,logical,numeric,numeric-method removeLinker,XStringSet,DNAString,missing,missing,missing-method |
| Retrieve NimbleGen's sequence capture linkers | sequenceCaptureLinkers sequenceCaptureLinkers,character-method sequenceCaptureLinkers,missing-method |
| A Histogram Of The Sequence Qualities | sequenceQualityHist sequenceQualityHist,QualityScaledDNAStringSet-method sequenceQualityHist,SFFContainer-method sequenceQualityHist,ShortReadQ-method |
| Filters output of variant information | setVariantFilter |
| Write A SFFContainer Object To A FASTQ File | sff2fastq sff2fastq,SFFContainer-method |
| Class '"SFFContainer"' | addRead addRead,SFFContainer,SFFRead-method clipAdapterLeft clipAdapterLeft,SFFContainer-method clipAdapterLeft<- clipAdapterLeft<-,SFFContainer,numeric-method clipAdapterRight clipAdapterRight,SFFContainer-method clipAdapterRight<- clipAdapterRight<-,SFFContainer,numeric-method clipQualityLeft clipQualityLeft,SFFContainer-method clipQualityLeft<- clipQualityLeft<-,SFFContainer,numeric-method clipQualityRight clipQualityRight,SFFContainer-method clipQualityRight<- clipQualityRight<-,SFFContainer,numeric-method flowChars flowChars,SFFContainer-method flowChars<- flowChars<-,SFFContainer,character-method flowgramFormat flowgramFormat,SFFContainer-method flowgramFormat<- flowgramFormat<-,SFFContainer,numeric-method flowgrams flowgrams,SFFContainer-method flowgrams<- flowgrams<-,SFFContainer,list-method flowIndexes flowIndexes,SFFContainer-method flowIndexes<- flowIndexes<-,SFFContainer,list-method getRead getRead,SFFContainer,character-method keySequence keySequence,SFFContainer-method keySequence<- keySequence<-,SFFContainer,character-method name name,SFFContainer-method name<- name<-,SFFContainer,character-method reads reads,SFFContainer-method reads<- reads<-,SFFContainer,QualityScaledDNAStringSet-method SFFContainer SFFContainer-class [,SFFContainer,ANY,ANY,ANY-method [,SFFContainer,ANY,ANY-method |
| Class '"SFFRead"' | clipAdapterLeft,SFFRead-method clipAdapterLeft<-,SFFRead,numeric-method clipAdapterRight,SFFRead-method clipAdapterRight<-,SFFRead,numeric-method clipQualityLeft,SFFRead-method clipQualityLeft<-,SFFRead,numeric-method clipQualityRight,SFFRead-method clipQualityRight<-,SFFRead,numeric-method flowChars,SFFRead-method flowChars<-,SFFRead,character-method flowgram flowgram,SFFRead-method flowgram<- flowgram<-,SFFRead,numeric-method flowgramFormat,SFFRead-method flowgramFormat<-,SFFRead,numeric-method flowIndexes,SFFRead-method flowIndexes<-,SFFRead,numeric-method keySequence,SFFRead-method keySequence<-,SFFRead,character-method name,SFFRead-method name<-,SFFRead,character-method quality,SFFRead-method quality<- quality<-,SFFRead,BString-method read read,SFFRead-method read<- read<-,SFFRead,QualityScaledDNAStringSet-method SFFRead SFFRead-class |
| Example data for 'plotVariants' | variants |
| Function To Write Files In Roche's .sff Format | writeSFF |