hictkR

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/hictkR@v0.0.3")

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},
}