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 |
computeNucleosomeEnrichmentOverBackground | Internal function |
computeVmat | A function to compute Vplot matrix |
CTCF_hg38 | CTCF_hg38 |
deconvolveBidirectionalPromoters | A function to duplicate bi-directional GRanges |
getCuts | Internal function |
getFragmentsDistribution | A function to compute sizes distribution for paired-end... |
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... |
nucleosomeEnrichment.GRanges | A function to compute nucleosome enrichment over a set of... |
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... |
shuffleVmat | A function to shuffle a Vmat |
theme_ggplot2 | Personal ggplot2 theming function, adapted from... |
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