# Set of tools to make V-plots and compute footprint profiles

## Documentation for package ‘VplotR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ABF1_sacCer3 | ABF1_sacCer3
alignToTSS | A function to re-align a GRanges object to TSSs
ATAC_ce11_Serizay2020 | ATAC_ce11_Serizay2020
bam_test | bam_test
ce11_all_REs | ce11_all_REs
ce11_proms | ce11_proms
computeVmat | A function to compute Vplot matrix
CTCF_hg38 | CTCF_hg38
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
MNase_sacCer3_Henikoff2011 | MNase_sacCer3_Henikoff2011
MNase_sacCer3_Henikoff2011_subset | MNase_sacCer3_Henikoff2011_subset
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.default | A function to plot a computed Vmat
plotVmat.GRanges | A function to compute (and plot) a Vmat
plotVmat.list | A function to compute (and plot) several Vmats.
plotVmat.Vmat | A function to plot a computed Vmat
plotVmat.VmatList | A function to plot a computed VmatList
REB1_sacCer3 | REB1_sacCer3
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/