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

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Files in this package

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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