HicAggR

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

Set of 3D genomic interaction analysis tools

Bioconductor version: Development (3.21)

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] (ORCID: ), David Depierre [aut], Naomi Schickele [ctb], Nicolas Chanard [aut], Refka Askri [ctb], Stéphane Schaak [aut, ctb], Pascal Martin [ctb], Olivier Cuvier [cre, ctb] (ORCID: )

Maintainer: Olivier Cuvier <olivier.cuvier at univ-tlse3.fr>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HicAggR")

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

Documentation

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

browseVignettes("HicAggR")

HicAggR - In depth tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, ChIPSeq, DNA3DStructure, DNaseSeq, DataImport, DataRepresentation, HiC, Normalization, RNASeq, Software, Visualization
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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
System Requirements
URL	https://bioconductor.org/packages/HicAggR https://cuvierlab.github.io/HicAggR/ https://github.com/CuvierLab/HicAggR
Bug Reports	https://github.com/CuvierLab/HicAggR/issues

Suggests	covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache(>= 2.6.1)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HicAggR_1.3.0.tar.gz
Windows Binary (x86_64)	HicAggR_1.3.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/HicAggR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HicAggR
Bioc Package Browser	https://code.bioconductor.org/browse/HicAggR/
Package Short Url	https://bioconductor.org/packages/HicAggR/
Package Downloads Report	Download Stats