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

checkRestrictionEnzymeSequenceRemove invalid 4C-seq reads from a SAM file
chooseNearCisFragmentsChoose fragments in a provided region around the viewpoint
createVirtualFragmentLibraryCreate a virtual fragment library from a provided genome and...
Data4CseqCreating a Data4Cseq object
Data4Cseq-classClass '"Data4Cseq"'
drawDigestionFragmentHistogramVisualize digestion fragments with a histogram
drawHeatmapDraw a heatmap-like multi-scale contact profile
exportVisualizationFragmentDataExport near-cis fragment data of a 'Data4Cseq' object
getReadDistributionCalculate the read distribution for a 4C-seq experiment
giveEnzymeSequenceProvide the corresponding enzyme sequence for an enzyme name
importVisualizationFragmentDataImport visualization data from a file
liverDataExample 4C-seq data set of fetal liver data
liverDataRawExample 4C-seq data set of fetal liver data
normalizeFragmentDataNormalize near-cis fragment data read count
plotTransInteractionsVisualize trans interaction intervals
prepare4CseqDataAlignment and filtering of raw 4C-seq data
printBEDFragmentLibraryPrint a BED-file fragment library
printWigFilePrint a wig file from 4C-seq read data
readPointsOfInterestFileRead a file with coordinates of marker points
readsToFragmentsDetermine fragment coverage of a 4C-seq fragment library
simulateDigestionSimulate the digestion of a genome
visualizeViewpointDraw a near-cis coverage plot for 4C-seq data
Basic4Cseq documentation built on May 2, 2018, 4:10 a.m.