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Bioconductor - HicAggR (development version)

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 (3.22)

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: 0000-0003-2358-219X , David Depierre [aut], Naomi Schickele [ctb], Nicolas Chanard [aut], Refka Askri [ctb], Stéphane Schaak [aut, ctb], Pascal Martin [ctb], Olivier Cuvier [cre, ctb] ORCID: 0000-0003-0644-2734

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")
Details biocViews ATACSeq, ChIPSeq, DNA3DStructure, DNaseSeq, DataImport, DataRepresentation, HiC, Normalization, RNASeq, Software, Visualization Version 1.5.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) 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 Package Archives

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

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