AccMatrix-class | AccMatrix class that is used to store accessibility matrices |
compareCorCoeffs | This function returns p-values assessing the difference... |
compareCorDistributions | This function returns p-values assessing the difference... |
CorMatrix-class | CorMatrix class that is used to store correlation matrices |
countReads | This function counts reads in a GRanges object that fall into... |
cropAccMatrix | This function crops accessibility matrices |
cropCorMatrix | This function crops correlation matrices |
getAccLUT | This function makes a color LUT for accessibility matrices |
getCIs | This function returns confidence intervals |
getCorBackground | This function returns the background correlation obtained... |
getCorLUT | This function makes a color LUT for correlation matrices |
getCorRanges | This function returns bootstrapped correlation coefficients |
getPEPairs | This function returns promoter-enhancer (P-E) pairs based on... |
makeAccMatrix | This function makes accessibility matrices from a set of BED... |
makeCorMatrix | This function makes a correlation matrix from two... |
makeGenomeTiles | This function makes tiles for the complete hg19 genome |
makeIPCHist | This function makes a histogram for the number of... |
makeIPCStats | Calculate statistics for the number of integrations per cell |
makeIPRHist | This function makes a histogram for the number of cells with... |
makeIPRStats | Calculate statistics for the number of integrations per ROI |
makeTiles | This function makes tiles for a particular chromosome of the... |
PEPairs-class | PEPairs class that is used to store sets of promoter-enhancer... |
readBed | This function reads a BED file and stores the reads in a... |
removeEmptyRows | This function removes empty rows from accessibility matrices |
removeRowsBelowCutoff | This function removes rows below a certain cutoff from... |
saveImage | This function saves a matrix as an image |
scaleAccMatrix | This function scales accessibility matrices to genomic... |
scaleCorMatrix | This function scales correlation matrices to genomic... |
writeMatrix | Wrapper for making and storing scaled corrleation matrices... |
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