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| 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/ |