Package: loopQTL Title: Anchor-Restricted Loop QTL Mapping from Hi-C Version: 0.99.0 Authors@R: c(person("Rhie Lab at the University of Southern California", email = "rhielab@gmail.com", role = "cre"), person("Zexun", "Wu", role = "aut", email = "zexunwu@usc.edu")) Description: Maps chromatin loop QTLs by testing whether genotype at a loop's anchors associates with the loop's contact strength across samples. Reads .hic files via strawr, builds an exact-coordinate consensus loop set, normalizes contact strength across samples via band-wise quantile normalization in the style of BNBC (implemented on top of preprocessCore), and runs anchor-restricted SNP-by-loop regressions with MatrixEQTL. Intra-chromosomal loops only; no FDR or lead-SNP selection (left to the user). URL: https://github.com/rhielab/loopQTL BugReports: https://github.com/rhielab/loopQTL/issues License: GPL-3 + file LICENSE Encoding: UTF-8 BiocType: Software biocViews: Software, DNA3DStructure, Epigenetics, HiC, QuantitativeTrailLocus, SNP Depends: R (>= 4.4) Imports: methods, stats, utils, strawr, preprocessCore, MatrixEQTL, GenomicRanges, IRanges, InteractionSet, S4Vectors, VariantAnnotation, Rsamtools, SummarizedExperiment, BiocParallel, data.table, ggplot2, scales, rtracklayer, patchwork Suggests: BiocStyle, knitr, rmarkdown VignetteBuilder: knitr Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 Config/roxygen2/version: 8.1.0 RoxygenNote: 7.3.3 Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev Repository: https://biocstaging.r-universe.dev Date/Publication: 2026-09-19 01:09:43 UTC RemoteUrl: https://github.com/BiocStaging/loopQTL RemoteRef: HEAD RemoteSha: cc881e77e9259e5461fd949c1420c9e47216bcec NeedsCompilation: no Packaged: 2026-09-19 06:08:48 UTC; root Author: Rhie Lab at the University of Southern California [cre], Zexun Wu [aut] Maintainer: Rhie Lab at the University of Southern California