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This is the development version of HicAggR; for the stable release version, see HicAggR.

Set of 3D genomic interaction analysis tools

Bioconductor version: Development (3.20)

This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values.

Author: Robel Tesfaye [aut, ctb] , David Depierre [aut], Naomi Schickele [ctb], Nicolas Chanard [aut], Refka Askri [ctb], St├ęphane Schaak [aut, ctb], Pascal Martin [ctb], Olivier Cuvier [cre, ctb]

Maintainer: Olivier Cuvier <olivier.cuvier at>

Citation (from within R, enter citation("HicAggR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

HicAggR - In depth tutorial HTML R Script
Reference Manual PDF


biocViews ATACSeq, ChIPSeq, DNA3DStructure, DNaseSeq, DataImport, DataRepresentation, HiC, Normalization, RNASeq, Software, Visualization
Version 1.1.2
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports InteractionSet, BiocGenerics, BiocParallel, dplyr, GenomeInfoDb, GenomicRanges, ggplot2, grDevices, IRanges, Matrix, methods, rhdf5, rlang, rtracklayer, S4Vectors, stats, utils, strawr, tibble, stringr, tidyr, gridExtra, data.table, reshape, checkmate, purrr, withr
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Suggests covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache(>= 2.6.1)
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Follow Installation instructions to use this package in your R session.

Source Package HicAggR_1.1.2.tar.gz
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macOS Binary (x86_64) HicAggR_1.1.2.tgz
macOS Binary (arm64) HicAggR_1.1.2.tgz
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