Package: looplook
Title: Integrative Suite for Target Assignment and Functional
        Annotation of Chromatin Interactions
Version: 0.99.12
Authors@R: c(
    person(given = "Ying", family = "ZHANG", 
           role = c("aut", "cre"), 
           email = "12207129@zju.edu.cn", 
           comment = c(ORCID = "0009-0005-9644-7062")),
    person(given = "Xingze", family = "HUANG",
           role = c("ctb"),
           email = "22407026@zju.edu.cn",
           comment = c(ORCID = "0009-0002-9286-1344")),
    person(given = "Ye", family = "CHEN",
           role = "ctb",
           email = "chenyephd@zju.edu.cn"),
    person(given = "Liang", family = "XU",
           role = c("ctb", "fnd"), 
           email = "xuliang.phd@zju.edu.cn",
           comment = "This work is funded by the Fundamental Research Funds for the Central Universities (226-2025-00101) and the National Natural Science Foundation of China (32270746, 82203247, 82203415).")
  )
Description: Provides a versatile suite for target assignment and functional
    annotation of 3D chromatin interactions. Leverages customizable genomic feature
    integration, expression-aware refinement, and connected-components clustering
    to prioritize biologically relevant chromatin loops. The pipeline also
    supports multi-omics data integration, functional annotation (GO, GSEA,
    motif, PPI), and publication-ready visualization.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
biocViews: Software, Epigenetics, HiC, ChIPSeq, RNASeq, GeneExpression,
        FunctionalGenomics, GenomeAnnotation, SystemsBiology,
        Visualization, Classification, Clustering, QualityControl,
        Spatial, Network, Coverage, GeneTarget
Depends: R (>= 4.5.0)
Imports: dplyr, ggplot2, tidyr, GenomicRanges, IRanges, S4Vectors,
        GenomeInfoDb, openxlsx, stats, utils, AnnotationDbi,
        GenomicFeatures, InteractionSet, RColorBrewer, UpSetR,
        data.table, fields, ggforce, ggrepel, igraph, karyoploteR,
        ChIPseeker, methods, scales, rlang
Suggests: BiocStyle, ComplexHeatmap, circlize, motifmatchr, JASPAR2020,
        TFBSTools, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10,
        BSgenome.Mmusculus.UCSC.mm9, ggseqlogo, STRINGdb, ggraph,
        enrichplot, clusterProfiler, aplot, ggtext, ggpointdensity, DT,
        viridis, ggpubr, ggdist, kableExtra, knitr, rmarkdown, png,
        BSgenome, htmltools, htmlwidgets, networkD3, webshot2,
        TxDb.Hsapiens.UCSC.hg38.knownGene,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene,
        TxDb.Mmusculus.UCSC.mm9.knownGene, org.Hs.eg.db, org.Mm.eg.db,
        testthat
URL: https://github.com/zying106/looplook,
        https://zying106.github.io/looplook/
BugReports: https://github.com/zying106/looplook/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-05-11 15:02:32 UTC; pkgbuild
Author: Ying ZHANG [aut, cre] (ORCID: <https://orcid.org/0009-0005-9644-7062>),
  Xingze HUANG [ctb] (ORCID: <https://orcid.org/0009-0002-9286-1344>),
  Ye CHEN [ctb],
  Liang XU [ctb, fnd] (This work is funded by the Fundamental Research
    Funds for the Central Universities (226-2025-00101) and the
    National Natural Science Foundation of China (32270746, 82203247,
    82203415).)
Maintainer: Ying ZHANG <12207129@zju.edu.cn>
