HicAggR
Set of 3D genomic interaction analysis tools
Bioconductor version: Release (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], Stéphane Schaak [aut, ctb], Pascal Martin [ctb], Olivier Cuvier [cre, ctb]
Maintainer: Olivier Cuvier <olivier.cuvier at univ-tlse3.fr>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, ChIPSeq, DNA3DStructure, DNaseSeq, DataImport, DataRepresentation, HiC, Normalization, RNASeq, Software, Visualization |
| Version | 1.2.0 |
| 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 |
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_1.2.0.tar.gz |
| Windows Binary (x86_64) | HicAggR_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | HicAggR_1.2.0.tgz |
| macOS Binary (arm64) | HicAggR_1.1.2.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 |