Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

AuthorCarolin Walter
Date of publicationNone
MaintainerCarolin Walter <carolin.walter@uni-muenster.de>
LicenseLGPL-3
Version1.10.0

View on Bioconductor

Functions

checkRestrictionEnzymeSequence Man page
checkRestrictionEnzymeSequence,character,character-method Man page
chooseNearCisFragments Man page
chooseNearCisFragments,Data4Cseq,numeric-method Man page
createVirtualFragmentLibrary Man page
createVirtualFragmentLibrary,BSgenome,character,character,numeri Man page
createVirtualFragmentLibrary,DNAString,character,character,numer Man page
Data4Cseq Man page
Data4Cseq,character,numeric,numeric,data.frame,GAlignments-metho Man page
Data4Cseq,character,numeric,numeric,missing,missing-method Man page
Data4Cseq-class Man page
drawDigestionFragmentHistogram Man page
drawDigestionFragmentHistogram,data.frame-method Man page
drawHeatmap Man page
drawHeatmap,Data4Cseq-method Man page
drawHeatmap,data.frame-method Man page
exportVisualizationFragmentData Man page
exportVisualizationFragmentData,Data4Cseq,character-method Man page
getReadDistribution Man page
getReadDistribution,Data4Cseq-method Man page
giveEnzymeSequence Man page
giveEnzymeSequence,character,character-method Man page
importVisualizationFragmentData Man page
importVisualizationFragmentData,character-method Man page
liverData Man page
liverDataRaw Man page
nearCisFragments Man page
nearCisFragments<- Man page
nearCisFragments<-,Data4Cseq,data.frame-method Man page
nearCisFragments,Data4Cseq-method Man page
normalizeFragmentData Man page
normalizeFragmentData,Data4Cseq-method Man page
plotTransInteractions Man page
plotTransInteractions,character,character,numeric,character-meth Man page
plotTransInteractions,data.frame,character,numeric,data.frame-me Man page
pointsOfInterest Man page
pointsOfInterest<- Man page
pointsOfInterest<-,Data4Cseq,data.frame-method Man page
pointsOfInterest,Data4Cseq-method Man page
prepare4CseqData Man page
prepare4CseqData,character,character,character,character-method Man page
printBEDFragmentLibrary Man page
printBEDFragmentLibrary,character,character-method Man page
printWigFile Man page
printWigFile,Data4Cseq-method Man page
rawFragments Man page
rawFragments<- Man page
rawFragments<-,Data4Cseq,data.frame-method Man page
rawFragments,Data4Cseq-method Man page
rawReads Man page
rawReads<- Man page
rawReads<-,Data4Cseq,GAlignments-method Man page
rawReads,Data4Cseq-method Man page
readLength Man page
readLength<- Man page
readLength,Data4Cseq-method Man page
readLength<-,Data4Cseq,numeric-method Man page
readPointsOfInterestFile Man page
readPointsOfInterestFile,character-method Man page
readsToFragments Man page
readsToFragments,Data4Cseq,character-method Man page
simulateDigestion Man page
simulateDigestion,character,character,BSgenome-method Man page
simulateDigestion,character,character,character-method Man page
viewpointChromosome Man page
viewpointChromosome<- Man page
viewpointChromosome<-,Data4Cseq,character-method Man page
viewpointChromosome,Data4Cseq-method Man page
viewpointInterval Man page
viewpointInterval<- Man page
viewpointInterval,Data4Cseq-method Man page
viewpointInterval<-,Data4Cseq,numeric-method Man page
visualizeViewpoint Man page
visualizeViewpoint,Data4Cseq-method Man page
visualizeViewpoint,data.frame-method Man page

Files

Basic4Cseq/DESCRIPTION
Basic4Cseq/NAMESPACE
Basic4Cseq/R
Basic4Cseq/R/AllClasses.r
Basic4Cseq/R/AllGenerics.r
Basic4Cseq/R/checkRestrictionEnzymeSequence.r
Basic4Cseq/R/chooseNearCisFragments.r
Basic4Cseq/R/createVirtualFragmentLibrary.r
Basic4Cseq/R/drawHeatmap.r
Basic4Cseq/R/formatFragmentData.r
Basic4Cseq/R/getReadDistribution.r
Basic4Cseq/R/giveEnzymeSequence.r
Basic4Cseq/R/methods-Data4Cseq.r
Basic4Cseq/R/normalizeFragmentData.r
Basic4Cseq/R/plotTransInteractions.r
Basic4Cseq/R/prepare4CseqData.r
Basic4Cseq/R/printBEDFragmentLibrary.r
Basic4Cseq/R/printWigFile.r
Basic4Cseq/R/readPointsOfInterestFile.r
Basic4Cseq/R/readsToFragments.r
Basic4Cseq/R/simulateDigestion.r
Basic4Cseq/R/visualizeViewpoint.r
Basic4Cseq/build
Basic4Cseq/build/vignette.rds
Basic4Cseq/data
Basic4Cseq/data/liverData.RData
Basic4Cseq/data/liverDataRaw.RData
Basic4Cseq/inst
Basic4Cseq/inst/doc
Basic4Cseq/inst/doc/vignette.R
Basic4Cseq/inst/doc/vignette.Rnw
Basic4Cseq/inst/doc/vignette.pdf
Basic4Cseq/inst/extdata
Basic4Cseq/inst/extdata/RCircos_GRCm38_ideogram.csv
Basic4Cseq/inst/extdata/RCircos_HG19_ideogram.csv
Basic4Cseq/inst/extdata/enzymeData.csv
Basic4Cseq/inst/extdata/fetalLiverCutter.sam
Basic4Cseq/inst/extdata/fetalLiverShort.bam
Basic4Cseq/inst/extdata/fetalLiverVP.bed
Basic4Cseq/inst/extdata/fetalLiver_finalFragments.csv
Basic4Cseq/inst/extdata/transInteractionData.txt
Basic4Cseq/inst/extdata/veryShortExample.fastq
Basic4Cseq/inst/extdata/veryShortLib.csv
Basic4Cseq/inst/extdata/veryShortReference.fasta
Basic4Cseq/inst/extdata/veryShortReference.fasta.amb
Basic4Cseq/inst/extdata/veryShortReference.fasta.ann
Basic4Cseq/inst/extdata/veryShortReference.fasta.bwt
Basic4Cseq/inst/extdata/veryShortReference.fasta.pac
Basic4Cseq/inst/extdata/veryShortReference.fasta.sa
Basic4Cseq/inst/extdata/vfl_aagctt_catg_mm9_54_vp.csv
Basic4Cseq/man
Basic4Cseq/man/Data4Cseq-class.Rd Basic4Cseq/man/Data4Cseq.Rd Basic4Cseq/man/checkRestrictionEnzymeSequence.Rd Basic4Cseq/man/chooseNearCisFragments.Rd Basic4Cseq/man/createVirtualFragmentLibrary.Rd Basic4Cseq/man/drawDigestionFragmentHistogram.Rd Basic4Cseq/man/drawHeatmap.Rd Basic4Cseq/man/exportVisualizationFragmentData.Rd Basic4Cseq/man/getReadDistribution.Rd Basic4Cseq/man/giveEnzymeSequence.Rd Basic4Cseq/man/importVisualizationFragmentData.Rd Basic4Cseq/man/liverData.Rd Basic4Cseq/man/liverDataRaw.Rd Basic4Cseq/man/normalizeFragmentData.Rd Basic4Cseq/man/plotTransInteractions.Rd Basic4Cseq/man/prepare4CseqData.Rd Basic4Cseq/man/printBEDFragmentLibrary.Rd Basic4Cseq/man/printWigFile.Rd Basic4Cseq/man/readPointsOfInterestFile.Rd Basic4Cseq/man/readsToFragments.Rd Basic4Cseq/man/simulateDigestion.Rd Basic4Cseq/man/visualizeViewpoint.Rd
Basic4Cseq/vignettes
Basic4Cseq/vignettes/images
Basic4Cseq/vignettes/images/drawHeatmap_Output.pdf
Basic4Cseq/vignettes/images/visualizeViewpoint_Output.pdf
Basic4Cseq/vignettes/vignette.Rnw

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