{ "_id": "6a17e719acfb0bcc41da171e", "Package": "damidBind", "Type": "Package", "Title": "Differential Binding and Expression Analysis for DamID-seq Data", "Version": "1.1.0", "Authors@R": "person(\"Owen\", \"Marshall\",\nemail = \"owen.marshall@utas.edu.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-1605-3871\"))", "Description": "The damidBind package provides a straightforward formal\nanalysis pipeline to analyse and explore differential DamID\nbinding, gene transcription or chromatin accessibility between\ntwo conditions. The package imports processed data from\nDamID-seq experiments, either as external raw files in the form\nof binding bedGraphs and GFF/BED peak calls, or as internal\nlists of GRanges objects. After optionally normalising data,\ncombining peaks across replicates and determining per-replicate\npeak occupancy, the package links bound loci to nearby genes.\nFor RNA Polymerase DamID data, the package calculates occupancy\nover genes, and optionally calcualates the FDR of\nsignificantly-enriched gene occupancy. damidBind then uses\neither limma (for conventional log2 ratio DamID binding data)\nor NOIseq (for counts-based CATaDa chromatin accessibility\ndata) to identify differentially-enriched regions, or\ndifferentially epxressed genes, between two conditions. The\npackage provides a number of visualisation tools (volcano\nplots, Gene Ontology enrichment plots via ClusterProfiler and\nproportional Venn diagrams via BioVenn for downstream data\nexploration and analysis. An powerful, interactive IGV genome\nbrowser interface (powered by Shiny and igvShiny) allows users\nto rapidly and intuitively assess significant\ndifferentially-bound regions in their genomic context.", "License": "GPL-3", "Encoding": "UTF-8", "biocViews": "DifferentialExpression, GeneExpression, Transcription,\nEpigenetics, Visualization, Sequencing, Software,\nGeneRegulation", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://marshall-lab.org/damidBind", "BugReports": "https://github.com/marshall-lab/damidBind/issues", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl libnode-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:06:03 UTC", "RemoteUrl": "https://github.com/bioc/damidBind", "RemoteRef": "HEAD", "RemoteSha": 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