{ "_id": "6a1ed610b401979e7340e8ec", "Package": "ttScreening", "Title": "Genome-Wide DNA Methylation Sites Screening by Use of Training\nand Testing Samples", "Version": "1.8", "Authors@R": "c(person(given=\"Meredith\", family=\"Ray\", email=\"maray@memphis.edu\", role = c(\"aut\", \"cre\")),\nperson(given=\"Mohammad Nahian Ferdous\", family=\"Abrar\", email=\"abrar0708@gmail.com\",role=c(\"aut\")), person(given=\"Yu\", family=\"Jiang\", role = c(\"aut\")),person(given=\"Xin\", family=\"Tong\", role = c(\"aut\")), person(given=\"Hongmei\", family=\"Zhang\", role = c(\"aut\")))", "Description": "A screening process utilizing training and testing samples\nto filter out uninformative DNA methylation sites. Surrogate\nvariables (SVs) of DNA methylation are included in the\nfiltering process to explain unknown factor effects. This\npackage also provides two screening functions for screening\nhigh-dimensional predictors when the events are rare. The firth\nmethod is called 'Rare-Screening' which employs a repeated\nrandom sampling with replacement and using linear modeling with\nBayes adjustment. The Second method is called\n'Firth-ttScreening' which uses 'ttScreening' method with\nadditional Firth correction term in the maximum likelihood for\nthe logistic regression model. These methods handle the\nhigh-dimensionality and low event rates.", "License": "Artistic-2.0", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "biocViews": "", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 10:24:21 UTC", "User": "root" }, "Author": "Meredith Ray [aut, cre], Mohammad Nahian Ferdous Abrar [aut],\nYu Jiang [aut], Xin Tong [aut], Hongmei Zhang [aut]", "Maintainer": "Meredith Ray ", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-01-30 17:50:02 UTC", "RemoteUrl": "https://github.com/cran/ttScreening", "RemoteRef": "HEAD", "RemoteSha": "7b199c76ef113c24a15c00544bd579414eba5e66", "MD5sum": "ec9e39edd93dd1195a961da1382c3650", "_user": "cran", "_type": "src", "_file": "ttScreening_1.8.tar.gz", "_fileid": "62489f3fedcdba4f289521adf4115cddf6d46b0321ca97d8032dfa2a73090565", "_filesize": 138292, "_sha256": "62489f3fedcdba4f289521adf4115cddf6d46b0321ca97d8032dfa2a73090565", "_created": "2026-05-20T10:24:21.000Z", "_published": "2026-06-02T13:09:36.748Z", "_distro": "noble", "_jobs": [ { "job": 79077805383, "time": 213, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7107511916" }, { "job": 79077805463, "time": 220, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7107514391" }, { "job": 79077805429, "time": 194, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7107442510" }, { "job": 79077804492, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7358555946" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26156381738", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/ttScreening", "_commit": { "id": "7b199c76ef113c24a15c00544bd579414eba5e66", "author": "Meredith Ray ", "committer": "cran-robot ", "message": "version 1.8\n", "time": 1769795402 }, "_maintainer": { "name": "Meredith Ray", "email": "maray@memphis.edu" }, "_registered": true, "_dependencies": [ { "package": "matrixStats", "role": "Depends" }, { "package": "sva", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "simsalapar", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "brglm2", "role": "Imports" }, { "package": "mvtnorm", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-27", "n": 1 }, { "week": "2026-05", "n": 1 } ], "_tags": [ { "name": "1.7", "date": "2025-07-03" }, { "name": "1.8", "date": "2026-01-30" } ], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 193, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ttScreening" }, "_mentions": 7, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ttScreening.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2013-10-05" }, { "version": "1.1", "date": "2013-10-06" }, { "version": "1.2", "date": "2013-10-08" }, { "version": "1.3", "date": "2014-02-28" }, { "version": "1.4", "date": "2014-08-29" }, { "version": "1.5", "date": "2014-11-14" }, { "version": "1.6", "date": "2018-10-11" }, { "version": "1.7", "date": "2025-07-03" }, { "version": "1.8", "date": "2026-01-30" } ], "_exports": [ "firth_screening", "irwsva.build2", "num.sv2", "Rare_Screening", "sva2", "ttScreening" ], "_help": [ { "page": "ttScreening-package", "title": "Genome-Wide DNA Methylation Sites Screening by Use of Training and Testing Samples", "topics": [ "ttScreening-package" ] }, { "page": "firth_screening", "title": "ttScreening with Firth bias-reduced logistic regression + multiple testing", "topics": [ "firth_screening" ] }, { "page": "irwsva.build2", "title": "Adjusted irwsva.build which builds surrogate variables from gene expression data", "topics": [ "irwsva.build2" ] }, { "page": "num.sv2", "title": "Adjusted num.sv which estimates the number of important surrogate variables from a gene expression data set.", "topics": [ "num.sv2" ] }, { "page": "Rare_Screening", "title": "Rare_Screening: resampling-based screening with limma", "topics": [ "Rare_Screening" ] }, { "page": "sva2", "title": "The adjusted sva code using irwsva.build2", "topics": [ "sva2" ] }, { "page": "ttScreening", "title": "A screening process built upon training and testing samples", "topics": [ "ttScreening" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "brglm2", "cachem", "cli", "codetools", "colorspace", "corpcor", "cpp11", "crayon", "curl", "DBI", "edgeR", "enrichwith", "fastmap", "formatR", "futile.logger", "futile.options", "genefilter", "generics", "glue", "gridBase", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nleqslv", "nlme", "nnet", "numDeriv", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "sfsmisc", "simsalapar", "snow", "statmod", "survival", "sva", "sys", "vctrs", "XML", "xtable", "XVector" ], "_score": 2.146128035678238, "_indexed": true, "_nocasepkg": "ttscreening", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8", "date": "2026-05-20T10:26:56.000Z", "distro": "noble", "commit": "7b199c76ef113c24a15c00544bd579414eba5e66", "fileid": "df2f30e57583e459312c94835e1deeae7d78076c6ed983b41c5b5f56f9a302be", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26156381738" }, { "r": "4.6.0", "os": "linux", "version": "1.8", "date": "2026-05-20T10:26:55.000Z", "distro": "noble", "commit": "7b199c76ef113c24a15c00544bd579414eba5e66", "fileid": "659a5c9a5c0a356a47db1619738da77ac999eca2f2d44afd7280c397e829a596", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26156381738" }, { "r": "4.6.0", "os": "wasm", "version": "1.8", "date": "2026-06-02T13:08:54.000Z", "commit": "7b199c76ef113c24a15c00544bd579414eba5e66", "fileid": "226cbe14e4236710b638b0bb36dcaa725b192c19baa695ae9c8006f11f20733a", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26156381738" } ] }