{ "_id": "6a494c83f6c47c441949968b", "Package": "preciseTAD", "Type": "Package", "Title": "preciseTAD: A machine learning framework for precise TAD\nboundary prediction", "Version": "1.23.0", "Authors@R": "c(\nperson(\"Spiro\", \"Stilianoudakis\",\nemail = \"stilianoudasc@vcu.edu\",\nrole = c(\"aut\")),\nperson(\"Mikhail\", \"Dozmorov\",\nemail = \"mikhail.dozmorov@gmail.com\",\nrole = c(\"aut\", \"cre\")))", "Description": "preciseTAD provides functions to predict the location of\nboundaries of topologically associated domains (TADs) and\nchromatin loops at base-level resolution. As an input, it takes\nBED-formatted genomic coordinates of domain boundaries detected\nfrom low-resolution Hi-C data, and coordinates of\nhigh-resolution genomic annotations from ENCODE or other\nconsortia. preciseTAD employs several feature engineering\nstrategies and resampling techniques to address class\nimbalance, and trains an optimized random forest model for\npredicting low-resolution domain boundaries. Translated on a\nbase-level, preciseTAD predicts the probability for each base\nto be a boundary. Density-based clustering and scalable\npartitioning techniques are used to detect precise boundary\nregions and summit points. Compared with low-resolution\nboundaries, preciseTAD boundaries are highly enriched for CTCF,\nRAD21, SMC3, and ZNF143 signal and more conserved across cell\nlines. The pre-trained model can accurately predict boundaries\nin another cell line using CTCF, RAD21, SMC3, and ZNF143\nannotation data for this cell line.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "biocViews": "Software, HiC, Sequencing, Clustering, Classification,\nFunctionalGenomics, FeatureExtraction", "BugReports": "https://github.com/dozmorovlab/preciseTAD/issues", "URL": "https://github.com/dozmorovlab/preciseTAD", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:42 UTC", "RemoteUrl": "https://github.com/bioc/preciseTAD", "RemoteRef": "HEAD", "RemoteSha": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 19:43:56 UTC", "User": "root" }, "Author": "Spiro Stilianoudakis 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