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Basic4Cseq (version 1.8.0)

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

Description

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.

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Version

Version

1.8.0

License

LGPL-3

Maintainer

Carolin Walter

Last Published

February 15th, 2017

Functions in Basic4Cseq (1.8.0)

visualizeViewpoint

Draw a near-cis coverage plot for 4C-seq data
chooseNearCisFragments

Choose fragments in a provided region around the viewpoint
exportVisualizationFragmentData

Export near-cis fragment data of a Data4Cseq object
readPointsOfInterestFile

Read a file with coordinates of marker points
importVisualizationFragmentData

Import visualization data from a file
Data4Cseq

Creating a Data4Cseq object
createVirtualFragmentLibrary

Create a virtual fragment library from a provided genome and two restriction enzymes
plotTransInteractions

Visualize trans interaction intervals
getReadDistribution

Calculate the read distribution for a 4C-seq experiment
liverData

Example 4C-seq data set of fetal liver data
normalizeFragmentData

Normalize near-cis fragment data read count
simulateDigestion

Simulate the digestion of a genome
Data4Cseq-class

Class "Data4Cseq"
liverDataRaw

Example 4C-seq data set of fetal liver data
drawDigestionFragmentHistogram

Visualize digestion fragments with a histogram
printWigFile

Print a wig file from 4C-seq read data
readsToFragments

Determine fragment coverage of a 4C-seq fragment library
printBEDFragmentLibrary

Print a BED-file fragment library
giveEnzymeSequence

Provide the corresponding enzyme sequence for an enzyme name
checkRestrictionEnzymeSequence

Remove invalid 4C-seq reads from a SAM file
drawHeatmap

Draw a heatmap-like multi-scale contact profile
prepare4CseqData

Alignment and filtering of raw 4C-seq data