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hictkR

License CI

R bindings for hictk, a blazing fast toolkit to work with .hic and .cool files.

Installing hictkR

hictkR can be installed directly from GitHub.

Installing hictkR requires a compiler toolchain supporting C++17, such as:

  • GCC 8+
  • Clang 8+
  • Apple-Clang 10.0+

On Windows a suitable compiler toolchain can be installed using Rtools.

Furthermore, the following tools are required:

  • CMake 3.25+
  • Conan 2+

Once all the build dependencies have been installed, the package can be installed as follows (note that this may require some time, as this involves the compilation of several packages):

install.packages("devtools")
devtools::install_github("paulsengroup/[email protected]")

Using hictkR

library(hictkR)

path <- "file.mcool"  # "file.hic"
f <- File(path, resolution=100000)

df <- fetch(f, "chr1:0-10,000,000", "chr2:0-20,000,000", join=TRUE)
df
chrom1 start1 end1 chrom2 start2 end2 count
chr1 0 100000 chr2 0 100000 15
chr1 0 100000 chr2 100000 200000 5
chr1 0 100000 chr2 300000 400000 17
chr1 0 100000 chr2 400000 500000 22
chr1 0 100000 chr2 500000 600000 30
chr1 0 100000 chr2 600000 700000 21
chr1 0 100000 chr2 600000 700000 21
... ... ... ... ... ... ...

Refer to the manual and vignette available at paulsengroup.github.io/hictkR for more examples on how to use hictkR.

Citing

If you use hictkR in you reaserch, please cite the following publication:

Roberto Rossini, Jonas Paulsen, hictk: blazing fast toolkit to work with .hic and .cool files Bioinformatics, Volume 40, Issue 7, July 2024, btae408, https://doi.org/10.1093/bioinformatics/btae408

BibTex 
@article{hictk,
    author = {Rossini, Roberto and Paulsen, Jonas},
    title = "{hictk: blazing fast toolkit to work with .hic and .cool files}",
    journal = {Bioinformatics},
    volume = {40},
    number = {7},
    pages = {btae408},
    year = {2024},
    month = {06},
    issn = {1367-4811},
    doi = {10.1093/bioinformatics/btae408},
    url = {https://doi.org/10.1093/bioinformatics/btae408},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/40/7/btae408/58385157/btae408.pdf},
}