Files in js2264/VplotR
Set of tools to make V-plots and compute footprint profiles
.Rbuildignore
.github/.gitignore
.github/workflows/rworkflows.yml
.github/workflows/test-coverage.yaml
.gitignore
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/bamutils.R
R/data.R
R/footprint.R
R/fragsize.R
R/globals.R
R/nucleosome_enrichment.R
R/utils.R
R/vmat.R
R/vmat_utils.R
R/vplot-chroms.R
README.md
codecov.yml
data/ABF1_sacCer3.rda
data/ATAC_ce11_Serizay2020.rda
data/CTCF_hg38.rda
data/MNase_sacCer3_Henikoff2011.rda
data/MNase_sacCer3_Henikoff2011_subset.rda
data/REB1_sacCer3.rda
data/bam_test.rda
data/ce11_all_REs.rda
data/ce11_proms.rda
inst/figures/concept.png
inst/figures/fragment_size_distribution.png
inst/figures/logo.png
inst/figures/vplot.png
man/ABF1_sacCer3.Rd
man/ATAC_ce11_Serizay2020.Rd
man/CTCF_hg38.Rd
man/MNase_sacCer3_Henikoff2011.Rd
man/MNase_sacCer3_Henikoff2011_subset.Rd
man/REB1_sacCer3.Rd
man/alignToTSS.Rd
man/bam_test.Rd
man/ce11_all_REs.Rd
man/ce11_proms.Rd
man/computeNucleosomeEnrichmentOverBackground.Rd
man/computeVmat.Rd
man/deconvolveBidirectionalPromoters.Rd
man/getCuts.Rd
man/getFragmentsDistribution.Rd
man/importPEBamFiles.Rd
man/normalizeVmat.Rd
man/nucleosomeEnrichment.GRanges.Rd
man/nucleosomeEnrichment.Rd
man/nucleosomeEnrichment.Vmat.Rd
man/plotFootprint.Rd
man/plotProfile.Rd
man/plotVmat.GRanges.Rd
man/plotVmat.Rd
man/plotVmat.Vmat.Rd
man/plotVmat.VmatList.Rd
man/plotVmat.default.Rd
man/plotVmat.list.Rd
man/sampleGRanges.GRanges.Rd
man/sampleGRanges.Rd
man/shiftATACGranges.Rd
man/shuffleVmat.Rd
man/theme_ggplot2.Rd
paper/figures/figures_example.png
paper/figures/figures_footprint.png
paper/figures/figures_fragsize.png
paper/figures/figures_locus.png
paper/figures/figures_vplot.png
paper/paper.bib
paper/paper.md
pkgdown/_pkgdown.yml
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/test-nucleosome-enrich.R
tests/testthat/test-vplot.R
vignettes/VplotR.Rmd
