ABF1_sacCer3            ABF1_sacCer3
ATAC_ce11_Serizay2020   ATAC_ce11_Serizay2020
CTCF_hg38               CTCF_hg38
MNase_sacCer3_Henikoff2011
                        MNase_sacCer3_Henikoff2011
MNase_sacCer3_Henikoff2011_subset
                        MNase_sacCer3_Henikoff2011_subset
REB1_sacCer3            REB1_sacCer3
alignToTSS              A function to re-align a GRanges object to TSSs
bam_test                bam_test
ce11_all_REs            ce11_all_REs
ce11_proms              ce11_proms
computeVmat             A function to compute Vplot matrix
deconvolveBidirectionalPromoters
                        A function to duplicate bi-directional GRanges
getFragmentsDistribution
                        A function to compute sizes distribution for
                        paired-end fragments
importPEBamFiles        A function to import paired end bam files as
                        GRanges
normalizeVmat           A function to normalized a Vmat
nucleosomeEnrichment    A function to compute nucleosome enrichment
                        over a set of GRanges
nucleosomeEnrichment.GRanges
                        A function to compute nucleosome enrichment
                        over a set of GRanges
nucleosomeEnrichment.Vmat
                        A function to compute nucleosome enrichment
                        over a Vmat
plotFootprint           A function to plot footprint of paired-end data
                        at given loci
plotProfile             A function to generate a Vplot along chromosome
                        coordinates
plotVmat                A function to generate a Vplot
plotVmat.GRanges        A function to compute (and plot) a Vmat
plotVmat.Vmat           A function to plot a computed Vmat
plotVmat.VmatList       A function to plot a computed VmatList
plotVmat.default        A function to plot a computed Vmat
plotVmat.list           A function to compute (and plot) several Vmats.
sampleGRanges           A function to sample GRanges from GRanges
sampleGRanges.GRanges   A function to sample GRanges within GRanges
shiftATACGranges        A function to shift GRanges fragments by 5/-4.
                        This is useful when dealing with fragments
                        coming from ATAC-seq.
shuffleVmat             A function to shuffle a Vmat
theme_ggplot2           Personal ggplot2 theming function, adapted from
                        roboto-condensed at
                        https://github.com/hrbrmstr/hrbrthemes/
