Registration Open for Bioc2024 July 24-26

HicAggR

Set of 3D genomic interaction analysis tools


Bioconductor version: Release (3.19)

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 univ-tlse3.fr>

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

Installation

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


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

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

Details

biocViews ATACSeq, ChIPSeq, DNA3DStructure, DNaseSeq, DataImport, DataRepresentation, HiC, Normalization, RNASeq, Software, Visualization
Version 1.0.2
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
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
See More
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_1.0.2.tar.gz
Windows Binary HicAggR_1.0.2.zip
macOS Binary (x86_64) HicAggR_1.0.2.tgz
macOS Binary (arm64) HicAggR_1.0.2.tgz
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
Old Source Packages for BioC 3.19 Source Archive