Awesome

NucleoATACR

R package for reading in and working with NucleoATAC outputs. This package doesn't replicate what NucleoATAC does-- just makes it easier to read in the outputs from NucleoATAC for visualizing and post-processing analysis in R.

Also includes functions for finding +1 and -1 nucleosomes, finding distances between nucleosomes, and plotting V-plots.

Install using devtools:

devtools::install_github("GreenleafLab/NucleoATACR")

Load:

library(NucleoATACR)

Read in nucleosome and nfr positions:

nucs <- readNucs("test.nucmap_combined.bed.gz")
nfrs <- readNFRs("test.nfrpos.bed.gz")

Read in nucleoatac signal track for particular locus:

signal <- readBedgraph("test.nucleoatac_signal.bedgraph.gz", "chrII", 706551, 707705)

Read in vplot and plot:

v <- read_vplot("test.VMat")
plotV(v)

Get +1 and -1 nucleosomes:

fake_tss <- GenomicRanges::GRanges("chrII", IRanges::IRanges(start = c(707200,707500), width = 1), 
              strand = c("+","-")) 
p1 <- get_p1_nuc(nucs.ranges = nucs, sites = fake_tss)
m1 <- get_m1_nuc(nucs.ranges = nucs, sites = fake_tss)