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.

Author
Carolin Walter
Date of publication
None
Maintainer
Carolin Walter <carolin.walter@uni-muenster.de>
License
LGPL-3
Version
1.10.0

View on Bioconductor

Man pages

checkRestrictionEnzymeSequence
Remove invalid 4C-seq reads from a SAM file
chooseNearCisFragments
Choose fragments in a provided region around the viewpoint
createVirtualFragmentLibrary
Create a virtual fragment library from a provided genome and...
Data4Cseq
Creating a Data4Cseq object
Data4Cseq-class
Class '"Data4Cseq"'
drawDigestionFragmentHistogram
Visualize digestion fragments with a histogram
drawHeatmap
Draw a heatmap-like multi-scale contact profile
exportVisualizationFragmentData
Export near-cis fragment data of a 'Data4Cseq' object
getReadDistribution
Calculate the read distribution for a 4C-seq experiment
giveEnzymeSequence
Provide the corresponding enzyme sequence for an enzyme name
importVisualizationFragmentData
Import visualization data from a file
liverData
Example 4C-seq data set of fetal liver data
liverDataRaw
Example 4C-seq data set of fetal liver data
normalizeFragmentData
Normalize near-cis fragment data read count
plotTransInteractions
Visualize trans interaction intervals
prepare4CseqData
Alignment and filtering of raw 4C-seq data
printBEDFragmentLibrary
Print a BED-file fragment library
printWigFile
Print a wig file from 4C-seq read data
readPointsOfInterestFile
Read a file with coordinates of marker points
readsToFragments
Determine fragment coverage of a 4C-seq fragment library
simulateDigestion
Simulate the digestion of a genome
visualizeViewpoint
Draw a near-cis coverage plot for 4C-seq data

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