{ "_id": "6a1abfd71d7bb097a09d6651", "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": "2026-05-30 07:12:15 UTC", "User": "root" }, "Author": "Spiro Stilianoudakis [aut],\nMikhail Dozmorov [aut, cre]", "Maintainer": "Mikhail Dozmorov ", "MD5sum": "b13a68d6340ba653da43ca2cbe551f0d", "_user": "bioc", "_type": "src", "_file": "preciseTAD_1.23.0.tar.gz", "_fileid": "f4df36d31a9876e6fe13d30a05f6c13df2fa5c35a16592016eddb4dbbc9d9013", "_filesize": 4233261, "_sha256": "f4df36d31a9876e6fe13d30a05f6c13df2fa5c35a16592016eddb4dbbc9d9013", "_created": "2026-05-30T07:12:15.000Z", "_published": "2026-05-30T10:45:42.991Z", "_jobs": [ { "job": 78632697123, "time": 337, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306404088" }, { "job": 78632697135, "time": 740, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306447808" }, { "job": 78632697125, "time": 886, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306465109" }, { "job": 78632697162, "time": 588, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307387581" }, { "job": 78632697193, "time": 615, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307389283" }, { "job": 78632186226, "time": 557, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306363913" }, { "job": 78632697122, "time": 282, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306397608" }, { "job": 78632697168, "time": 656, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306438729" }, { "job": 78632697140, "time": 664, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306439663" }, { "job": 78632697157, "time": 589, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306431906" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/preciseTAD", "_commit": { "id": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380822 }, "_maintainer": { "name": "Mikhail Dozmorov", "email": "mikhail.dozmorov@gmail.com", "login": "mdozmorov", "twitter": "@mikhaildozmorov", "description": "Bioinformatician, interested in 3D genomics, cancer, statistics, programming, machine and deep learning", "uuid": 864945 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "ModelMetrics", "role": "Imports" }, { "package": "e1071", "role": "Imports" }, { "package": "PRROC", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "dbscan", "role": "Imports" }, { "package": "doSNOW", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "rCGH", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocCheck", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "software", "hic", "sequencing", "clustering", "classification", "functionalgenomics", "featureextraction" ], "_stars": 8, "_contributors": [ { "user": "stilianoudakis", "count": 83, "uuid": 31807065 }, { "user": "mdozmorov", "count": 71, "uuid": 864945 }, { "user": "nturaga", "count": 6, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 373, "source": "https://www.bioconductor.org/packages/stats/bioc/preciseTAD" }, "_devurl": "https://github.com/dozmorovlab/precisetad", "_searchresults": 19, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/preciseTAD.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/dozmorovlab/precisetad", "_realowner": "bioc", "_cranurl": false, "_exports": [ "bedToGRangesList", "createTADdata", "extractBoundaries", "juicer_func", "preciseTAD", "TADrandomForest", "TADrfe" ], "_datasets": [ { "name": "arrowhead_gm12878_5kb", "title": "Domain data from ARROWHEAD TAD-caller for GM12878 at 5 kb", "object": "arrowhead_gm12878_5kb", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3" ], "rows": 8409, "table": true, "tojson": true }, { "name": "tfbsList", "title": "A list of the chromosomal coordinates for 26 transcription factor binding sites from the Gm12878 cell line", "object": "tfbsList", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "arrowhead_gm12878_5kb", "title": "Domain data from ARROWHEAD TAD-caller for GM12878 at 5 kb", "topics": [ "arrowhead_gm12878_5kb" ] }, { "page": "bedToGRangesList", "title": "Function to create a GRangesList object from functional genomic annotation data in the form of BED files", "topics": [ "bedToGRangesList" ] }, { "page": "binary_func", "title": "Helper function used to create binary overlap type feature space", "topics": [ "binary_func" ] }, { "page": "count_func", "title": "Helper function used to create count overlap type feature space", "topics": [ "count_func" ] }, { "page": "createTADdata", "title": "Function to create a data matrix used for building a predictive model to classify boundary regions from functional genomic elements", "topics": [ "createTADdata" ] }, { "page": "distance_func", "title": "Helper function used to create (log2) distance type feature space", "topics": [ "distance_func" ] }, { "page": "extractBoundaries", "title": "Function to extract boundaries from domain data.", "topics": [ "extractBoundaries" ] }, { "page": "juicer_func", "title": "Helper function for transforming a GRanges object into matrix form to be saved as .txt or .BED file and imported into juicer", "topics": [ "juicer_func" ] }, { "page": "percent_func", "title": "Helper function used to create percent overlap type feature space", "topics": [ "percent_func" ] }, { "page": "preciseTAD", "title": "Precise TAD boundary prediction at base-level resolution using density-based spatial clustering and partitioning techniques", "topics": [ "preciseTAD" ] }, { "page": "signal_func", "title": "Helper function used to create signal type feature space", "topics": [ "signal_func" ] }, { "page": "TADrandomForest", "title": "A wrapper function passed to 'caret::train' to apply a random forest classification algorithm built and tested on user-defined binned domain data from 'createTADdata'.", "topics": [ "TADrandomForest" ] }, { "page": "TADrfe", "title": "A wrapper function passed to 'caret::rfe' to apply recursive feature elimination (RFE) on binned domain data as a feature reduction technique for random forests. Backward elimination is performed from p down to 2, by powers of 2, where p is the number of features in the data.", "topics": [ "TADrfe" ] }, { "page": "tfbsList", "title": "A list of the chromosomal coordinates for 26 transcription factor binding sites from the Gm12878 cell line", "topics": [ "tfbsList" ] } ], "_readme": "https://github.com/bioc/preciseTAD/raw/HEAD/README.md", "_rundeps": [ "abind", "aCGH", "affy", "affyio", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "caret", "cigarillo", "class", "cli", "clock", "cluster", "codetools", "commonmark", "cpp11", "crayon", "curl", "data.table", "DBI", "dbscan", "DelayedArray", "diagram", "digest", "DNAcopy", "doSNOW", "dplyr", "e1071", "farver", "fastmap", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "globals", "glue", "gower", "gtable", "gtools", "hardhat", "htmltools", "httpuv", "httr", "ipred", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "labeling", "lambda.r", "later", "lattice", "lava", "lifecycle", "limma", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mime", "ModelMetrics", "multtest", "nlme", "nnet", "numDeriv", "openssl", "org.Hs.eg.db", "otel", "parallelly", "pbapply", "pillar", "pkgconfig", "plyr", "png", "preprocessCore", "pROC", "prodlim", "progressr", "promises", "proxy", "PRROC", "purrr", "R6", "randomForest", "rappdirs", "rCGH", "RColorBrewer", "Rcpp", "RCurl", "recipes", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "rpart", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shape", "shiny", "snow", "sourcetools", "SparseArray", "sparsevctrs", "SQUAREM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "TxDb.Hsapiens.UCSC.hg18.knownGene", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Hsapiens.UCSC.hg38.knownGene", "tzdb", "utf8", "vctrs", "viridisLite", "withr", "XML", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "preciseTAD.Rmd", "filename": "preciseTAD.html", "title": "preciseTAD Vignette", "author": "Spiro Stilianoudakis, Mikhail Dozmorov", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Input data", "preciseTAD functionality and output", "Getting Started", "Installation", "Implementation", "Model building", "Construction of the data matrix", "Feature selection using recursive feature elimination", "Implementing a random forest for boundary prediction", "Precise boundary prediction", "Running preciseTAD", "Using preciseTAD with Juicebox", "Cross-cell-type prediction", "References" ], "created": "2020-06-19 15:59:09", "modified": "2021-09-28 16:52:33", "commits": 45 } ], "_score": 5.482873583608754, "_indexed": true, "_nocasepkg": "precisetad", "_universes": [ "bioc", "mdozmorov", "dozmorovlab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T07:18:07.000Z", "distro": "noble", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "ee990a92338048b5e3c1b84babe9bd86a115d09c1f59b9fa20b29fa99f0a925c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T07:20:41.000Z", "distro": "noble", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "9d1fcf7bbaae739e66c9dfdf91bdefe3989988ebb72cfb095361c1e799b1eda8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-05-30T09:57:05.000Z", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "942bdddbcff033f4c8ff31db17bfffafd6de5aad32f8a117f28df786cc7ad1e6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-05-30T09:57:10.000Z", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "f9cd280c1e46a727a9ccca2f14213a9db7129f065908b2af1cb38d93a90725f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-05-30T07:17:44.000Z", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "1ea759bd9993b47117e2436921941de7b1bf6313f842310dcfd9df31d816ce4e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:15:53.000Z", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "918c7ee2a56cf9946ce987e749983cfb3505f2682329465b3267135d5c3c0563", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:15:55.000Z", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "2abb10b10005dbec5624b45b12b62c224b12cd49022adbcc89f6de8b84b50a65", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" }, { "r": "4.6.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:15:24.000Z", "commit": "9f07a14d91a01296708baf1bbb9854ec55c0872c", "fileid": "7e55bc0ad47070fe1a7f5f5c8fe0fae608083674aee613847109121b075068f2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677584782" } ] }