{ "_id": "6adf3935f24dcd7a258c8847", "Type": "Package", "Package": "HicAggR", "Title": "Set of 3D genomic interaction analysis tools", "Version": "1.9.0", "Authors@R": "c(\nperson(\"Robel\", \"Tesfaye\", email = \"rob.tesf@gmail.com\",\nrole = c(\"aut\",\"ctb\"), comment = c(ORCID=\"0000-0003-2358-219X\")),\nperson(\"David\", \"Depierre\", email = \"dav.depierre@gmail.com\",\nrole = \"aut\"),\nperson(\"Naomi\", \"Schickele\", email = \"naomi.schickele@univ-tlse3.fr\",\nrole = \"ctb\"),\nperson(\"Nicolas\", \"Chanard\", email = \"nico.chanard@gmail.com\",\nrole = \"aut\"),\nperson(\"Refka\", \"Askri\", email = \"refka.askri@univ-tlse3.fr\",\nrole = \"ctb\"),\nperson(\"Stéphane\", \"Schaak\", email = \"stephane.schaak@inserm.fr\",\nrole = c(\"aut\",\"ctb\")),\nperson(\"Pascal\", \"Martin\", email = \"pascal.martin@inra.fr\",\nrole = \"ctb\"),\nperson(\"Olivier\", \"Cuvier\", email = \"olivier.cuvier@univ-tlse3.fr\",\nrole = c(\"cre\",\"ctb\"), comment = c(ORCID=\"0000-0003-0644-2734\"))\n)", "Description": "This package provides a set of functions useful in the\nanalysis of 3D genomic interactions. It includes the import of\nstandard HiC data formats into R and HiC normalisation\nprocedures. The main objective of this package is to improve\nthe visualization and quantification of the analysis of HiC\ncontacts through aggregation. The package allows to import 1D\ngenomics data, such as peaks from ATACSeq, ChIPSeq, to create\npotential couples between features of interest under\nuser-defined parameters such as distance between pairs of\nfeatures of interest. It allows then the extraction of contact\nvalues from the HiC data for these couples and to perform\nAggregated Peak Analysis (APA) for visualization, but also to\ncompare normalized contact values between conditions. Overall\nthe package allows to integrate 1D genomics data with 3D\ngenomics data, providing an easy access to HiC contact values.", "biocViews": "Software, HiC, DataImport, DataRepresentation,\nNormalization, Visualization, DNA3DStructure, ATACSeq, ChIPSeq,\nDNaseSeq, RNASeq", "License": "MIT + file LICENSE", "URL": "https://bioconductor.org/packages/HicAggR,\nhttps://cuvierlab.github.io/HicAggR/,\nhttps://github.com/CuvierLab/HicAggR", "BugReports": "https://github.com/CuvierLab/HicAggR/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:09 UTC", "RemoteUrl": "https://github.com/bioc/HicAggR", "RemoteRef": "HEAD", "RemoteSha": "4fcc34f03ac7182b2a2a2a3aa1f49978bbbfe4d0", 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