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HawkGenomics website

R package to Estimate parameters for a hawkes model over spatial positions using this c++ implementation.


A C++ compiler supporting C++14 is required:

  • g++ >= 5.0
  • clang++ >= 3.4
  • for any other compiler, check that it supports the -std=c++14 flag

R >= 4.3 (the package may works on older version of R)


You need the package remotes to install hawkesGenomics from this repository


Then you can install hawkesGenomics with this command

remotes::install_git("", force = T)


We are going to analyse a subset of the replication origin on the chromosme 1 of hg19.


preprocess data

beds <- preprocess_bed(
  files = c(
    system.file("extdata", "oris.bed.gz", package = "hawkesGenomics"),
    system.file("extdata", "CGI.bed.gz", package = "hawkesGenomics"),
    system.file("extdata", "G4plus.bed.gz", package = "hawkesGenomics")
  names = c("Oris", "CGI", "G4plus")

hawkes computation

res <- compute_hawkes_histogram(
  files = beds$preprocess_beds,
  names = beds$names,
  K = 5,
  delta = 1e4

plot data

plot_histogram(res, K = 5, delta = 1e4)

plot_convolution(res, width = beds$interval_size, K = 5, delta = 1e4)