{ "_id": "6aca20c2fe5cc25786e8500d", "Package": "preciseTADhub", "Type": "Package", "Title": "Pre-trained random forest models obtained using preciseTAD", "Version": "1.20.0", "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": "An experimentdata package to supplement the preciseTAD\npackage containing pre-trained models and the variable\nimportances of each genomic annotation used to build the model\nparsed into list objects and available in ExperimentHub. In\ntotal, preciseTADhub provides access to n=84 random forest\nclassification models optimized to predict TAD/chromatin loop\nboundary regions and stored as .RDS files. The value, n, comes\nfrom the fact that we considered l=2 cell lines {GM12878,\nK562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and\nc=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting\nCHR9). Furthermore, each object is itself a two-item list\ncontaining: (1) the model object, and (2) the variable\nimportances for CTCF, RAD21, SMC3, and ZNF143 used to predict\nboundary regions. Each model is trained via a \"holdout\"\nstrategy, in which data from chromosomes {CHR1, CHR2, ...,\nCHRi-1, CHRi+1, ..., CHR22} were used to build the model and\nthe ith chromosome was reserved for testing. See\nhttps://doi.org/10.1101/2020.09.03.282186 for more detail on\nthe model building strategy.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "ExperimentData, PackageTypeData, ExperimentHub, Genome", "NeedsCompilation": "no", "RoxygenNote": "7.1.1", "BugReports": "https://github.com/dozmorovlab/preciseTADhub/issues", "URL": "https://github.com/dozmorovlab/preciseTADhub", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:34:36 UTC", "RemoteUrl": "https://github.com/bioc/preciseTADhub", "RemoteRef": "RELEASE_3_23", "RemoteSha": "591f5abbecd02cb98b8a0978c27d66b35d58ff26", "Packaged": { "Date": "2026-10-10 11:17:33 UTC", "User": "root" }, "Author": "Spiro Stilianoudakis [aut],\nMikhail Dozmorov [aut, cre]", "Maintainer": "Mikhail Dozmorov ", "_user": "bioc-release", "_type": "src", "_file": "preciseTADhub_1.20.0.tar.gz", "_fileid": 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