{ "_id": "6a10365bacfb0bcc41c9a026", "Package": "leapp", "Version": "1.3", "Date": "2022-06-19", "Title": "Latent Effect Adjustment After Primary Projection", "Author": "Yunting Sun , Nancy R.Zhang\n, Art B.Owen ", "Maintainer": "Yunting Sun ", "Description": "These functions take a gene expression value matrix, a\nprimary covariate vector, an additional known covariates\nmatrix. A two stage analysis is applied to counter the effects\nof latent variables on the rankings of hypotheses. The\nestimation and adjustment of latent effects are proposed by\nSun, Zhang and Owen (2011). \"leapp\" is developed in the\ncontext of microarray experiments, but may be used as a general\ntool for high throughput data sets where dependence may be\ninvolved.", "License": "GPL (>= 2)", "Packaged": { "Date": "2026-05-12 06:47:22 UTC", "User": "root" }, "NeedsCompilation": "no", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2022-06-19 20:10:02 UTC", "RemoteUrl": "https://github.com/cran/leapp", "RemoteRef": "HEAD", "RemoteSha": "bce08cc7d0b9e446288bbe81e9b38d31f511a0b5", "MD5sum": "e579fff4bbf5f53dc010d7f8abca9ede", "_user": "cran", "_type": "src", "_file": "leapp_1.3.tar.gz", "_fileid": "3077f15ec163432e6f909f67cdd4bb4e4738c06c1b5ecb78ab7ec00f248b99a7", "_filesize": 609609, "_sha256": "3077f15ec163432e6f909f67cdd4bb4e4738c06c1b5ecb78ab7ec00f248b99a7", "_created": "2026-05-12T06:47:22.000Z", "_published": "2026-05-22T10:56:27.789Z", "_distro": "noble", "_jobs": [ { "job": 77365738481, "time": 213, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6937524152" }, { "job": 77365738420, "time": 198, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6937518701" }, { "job": 77365738285, "time": 191, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6937467576" }, { "job": 77365737941, "time": 129, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7158825307" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25718175181", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/leapp", "_commit": { "id": "bce08cc7d0b9e446288bbe81e9b38d31f511a0b5", "author": "Yunting Sun ", "committer": "cran-robot ", "message": "version 1.3\n", "time": 1655669402 }, "_maintainer": { "name": "Yunting Sun", "email": "yunting.sun@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.1", "role": "Depends" }, { "package": "sva", "role": "Depends" }, { "package": "MASS", "role": "Depends" }, { "package": "corpcor", "role": "Depends" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 247, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/leapp" }, "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/leapp.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2012-04-07" }, { "version": "1.1", "date": "2014-01-06" }, { "version": "1.2", "date": "2014-07-22" }, { "version": "1.3", "date": "2022-06-19" } ], "_exports": [ "AlternateSVD", "FindAUC", "FindFpr", "FindPrec", "FindRec", "FindTpr", "IPOD", "IPODFUN", "leapp", "ridge", "ROCplot" ], "_datasets": [ { "name": "simdat", "title": "Simulated gene expression data affected by a group variable and an unobserved factor", "object": "simdat", "file": "simdat.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "leapp-package", "title": "latent effect adjustment after primary projection", "topics": [ "leapp-package" ] }, { "page": "AlternateSVD", "title": "Alternating singular value decomposition", "topics": [ "AlternateSVD" ] }, { "page": "FindAUC", "title": "Compute the area under the ROC curve (AUC)", "topics": [ "FindAUC" ] }, { "page": "FindFpr", "title": "Compute the false positive rate at given sizes of retrieved genes", "topics": [ "FindFpr" ] }, { "page": "FindPrec", "title": "compute the precision at given sizes of retrieved genes", "topics": [ "FindPrec" ] }, { "page": "FindRec", "title": "compute the recall at given sizes of retrieved genes", "topics": [ "FindRec" ] }, { "page": "FindTpr", "title": "compute the true positive rate at given sizes of retrieved genes", "topics": [ "FindTpr" ] }, { "page": "IPOD", "title": "Iterative penalized outlier detection algorithm", "topics": [ "IPOD" ] }, { "page": "IPODFUN", "title": "compute the iterative penalized outlier detection given the noise standard deviation sigma", "topics": [ "IPODFUN" ] }, { "page": "leapp", "title": "latent effect adjustment after primary projection", "topics": [ "leapp" ] }, { "page": "Pvalue", "title": "Calculate statistics and p-values", "topics": [ "Pvalue" ] }, { "page": "ridge", "title": "Outlier detection with a ridge penalty", "topics": [ "ridge" ] }, { "page": "ROCplot", "title": "plot ROC curve", "topics": [ "ROCplot" ] }, { "page": "simdat", "title": "Simulated gene expression data affected by a group variable and an unobserved factor", "topics": [ "simdat" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "corpcor", "cpp11", "crayon", "curl", "DBI", "edgeR", "fastmap", "formatR", "futile.logger", "futile.options", "genefilter", "generics", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "snow", "statmod", "survival", "sva", "sys", "vctrs", "XML", "xtable", "XVector" ], "_score": 1.0413926851582251, "_indexed": true, "_nocasepkg": "leapp", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3", "date": "2026-05-12T06:49:57.000Z", "distro": "noble", "commit": "bce08cc7d0b9e446288bbe81e9b38d31f511a0b5", "fileid": "6f7980c954a5fef0b0de492a44e53549260e26623be4809cd4ba610d26076c0a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/25718175181" }, { "r": "4.6.0", "os": "linux", "version": "1.3", "date": "2026-05-12T06:49:52.000Z", "distro": "noble", "commit": "bce08cc7d0b9e446288bbe81e9b38d31f511a0b5", "fileid": "c8f96f9812ae49be5480db70dddeedeba10b212d193677d4b525302c4155b91a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/25718175181" }, { "r": "4.6.0", "os": "wasm", "version": "1.3", "date": "2026-05-22T10:56:04.000Z", "commit": "bce08cc7d0b9e446288bbe81e9b38d31f511a0b5", "fileid": "008da3a63478ef5f7e2124b844911766d9884765d3685f830a0066c3a35b14b4", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25718175181" } ] }