{ "_id": "6a194ec8acfb0bcc41ddeb29", "Package": "miRLAB", "Type": "Package", "Title": "Dry lab for exploring miRNA-mRNA relationships", "Version": "1.42.0", "Date": "2021.10.07", "Author": "Thuc Duy Le, Junpeng Zhang, Mo Chen, Vu Viet Hoang Pham", "Maintainer": "Thuc Duy Le ", "Description": "Provide tools exploring miRNA-mRNA relationships,\nincluding popular miRNA target prediction methods, ensemble\nmethods that integrate individual methods, functions to get\ndata from online resources, functions to validate the results,\nand functions to conduct enrichment analyses.", "License": "GPL (>=2)", "VignetteBuilder": "knitr", "biocViews": "miRNA, GeneExpression, NetworkInference, Network", "RoxygenNote": "7.1.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:22:47 UTC", "User": "root" }, "URL": "https://github.com/pvvhoang/miRLAB", "Config/pak/sysreqs": "cmake libglpk-dev make libgsl0-dev libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:41:32 UTC", "RemoteUrl": "https://github.com/bioc/miRLAB", "RemoteRef": "RELEASE_3_23", "RemoteSha": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "MD5sum": "7a96f63d4ffd922c321876ebee428e8c", "_user": "bioc-release", "_type": "src", "_file": "miRLAB_1.42.0.tar.gz", "_fileid": "ae6736c0189dee7d4a44e81f38205080b1dbc43758e7c4a0c3a23c6553e08bc6", "_filesize": 349250, "_sha256": "ae6736c0189dee7d4a44e81f38205080b1dbc43758e7c4a0c3a23c6553e08bc6", "_created": "2026-05-29T07:22:47.000Z", "_published": "2026-05-29T08:31:04.089Z", "_jobs": [ { "job": 78456517660, "time": 283, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7285387997" }, { "job": 78456517604, "time": 457, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7285441130" }, { "job": 78456517568, "time": 460, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7285442270" }, { "job": 78456517655, "time": 214, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7286457098" }, { "job": 78456517584, "time": 248, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7286463542" }, { "job": 78455733066, "time": 349, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285303338" }, { "job": 78456517556, "time": 267, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285382587" }, { "job": 78456517615, "time": 377, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7285417069" }, { "job": 78456517650, "time": 338, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7285405215" }, { "job": 78456517676, "time": 332, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7285404470" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/miRLAB", "_commit": { "id": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380092 }, "_maintainer": { "name": "Thuc Duy Le", "email": "thuc.le@unisa.edu.au", "login": "thucduyle", "description": "", "uuid": 141245131 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "Hmisc", "role": "Imports" }, { "package": "energy", "role": "Imports" }, { "package": "entropy", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "impute", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "pcalg", "role": "Imports" }, { "package": "TCGAbiolinks", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "ctc", "role": "Imports" }, { "package": "InvariantCausalPrediction", "role": "Imports" }, { "package": "Category", "role": "Imports" }, { "package": "GOstats", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_topics": [ "mirna", "geneexpression", "networkinference", "network" ], "_stars": 0, "_contributors": [ { "user": "pvvhoang", "count": 34, "uuid": 40186759 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "thucduyle", "count": 7, "uuid": 141245131 }, { "user": "dtenenba", "count": 6, "uuid": 2286826 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 364, "source": "https://www.bioconductor.org/packages/stats/bioc/miRLAB" }, "_mentions": 4, "_devurl": "https://github.com/pvvhoang/mirlab", "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/miRLAB.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/pvvhoang/mirlab", "_realowner": "bioc", "_cranurl": false, "_exports": [ "Borda", "BordaTopk", "bRank", "convert", "Dcov", "DiffExpAnalysis", "Elastic", "experiment", "Extopk", "filterAndCompare", "getData", "GOBPenrichment", "Hoeffding", "ICPPam50", "IDA", "identifymiRTargetsByEnsemble", "identifymiRTargetsByICPPam50", "ImputeNormData", "KEGGenrichment", "Kendall", "Lasso", "MI", "Pearson", "RDC", "Read", "ReadExtResult", "readHeader", "Spearman", "ValidateAll", "Validation", "ValidationT", "Zscore" ], "_help": [ { "page": "miRLAB-package", "title": "A dry lab for exploring miRNA-mRNA relationships", "topics": [ "miRLAB-package", "miRLAB" ] }, { "page": "Borda", "title": "Ensemble method for miRNA target prediction using Borda count election", "topics": [ "Borda" ] }, { "page": "BordaTopk", "title": "Ensemble method for miRNA target prediction using Borda count election with topk targets", "topics": [ "BordaTopk" ] }, { "page": "bRank", "title": "Extract topk predicted targets of a miRNA Rank all the targets of a miRNA and extract the topk targets", "topics": [ "bRank" ] }, { "page": "convert", "title": "Convert miRNA symbols from a miRBase version to another", "topics": [ "convert" ] }, { "page": "Dcov", "title": "miRNA target prediction with the Distance correlation method", "topics": [ "Dcov" ] }, { "page": "DiffExpAnalysis", "title": "Differentially expressed analysis", "topics": [ "DiffExpAnalysis" ] }, { "page": "Elastic", "title": "miRNA target prediction with the Elastic-net regression coefficient method", "topics": [ "Elastic" ] }, { "page": "experiment", "title": "Function for validate the results from all 12 methods.", "topics": [ "experiment" ] }, { "page": "Extopk", "title": "Extract top k miRNA-mRNA interactions", "topics": [ "Extopk" ] }, { "page": "filterAndCompare", "title": "Filter and compare the validation results from 12 methods Keep the miRNAs that have at least noVal confirmed targets and compare the validation results from all methods.", "topics": [ "filterAndCompare" ] }, { "page": "getData", "title": "getData from GDC", "topics": [ "getData" ] }, { "page": "GOBPenrichment", "title": "Functional enrichment analysis", "topics": [ "GOBPenrichment" ] }, { "page": "Hoeffding", "title": "miRNA target prediction with the Hoeffding correlation coefficient method", "topics": [ "Hoeffding" ] }, { "page": "ICPPam50", "title": "Identify miRNA targets by ICP and PAM50", "topics": [ "ICPPam50" ] }, { "page": "IDA", "title": "miRNA target prediction with the IDA method", "topics": [ "IDA" ] }, { "page": "identifymiRTargetsByEnsemble", "title": "Identify the top miRNA targets by an ensemble method with ICP-PAM50, Pearson and Lasso", "topics": [ "identifymiRTargetsByEnsemble" ] }, { "page": "identifymiRTargetsByICPPam50", "title": "Identify the top miRNA targets by ICP and PAM50", "topics": [ "identifymiRTargetsByICPPam50" ] }, { "page": "ImputeNormData", "title": "Filter, impute, and normalise data.", "topics": [ "ImputeNormData" ] }, { "page": "KEGGenrichment", "title": "Functional enrichment analysis KEGG enrichment analysis for a gene list", "topics": [ "KEGGenrichment" ] }, { "page": "Kendall", "title": "miRNA target prediction with the Kendall correlation coefficient method", "topics": [ "Kendall" ] }, { "page": "Lasso", "title": "miRNA target prediction with the Lasso method", "topics": [ "Lasso" ] }, { "page": "MI", "title": "miRNA target prediction with mutual information method", "topics": [ "MI" ] }, { "page": "Pearson", "title": "miRNA target prediction with the Pearson correlation coefficient method", "topics": [ "Pearson" ] }, { "page": "RDC", "title": "miRNA target prediction with the Randomized Dependence Coefficient method", "topics": [ "RDC" ] }, { "page": "Read", "title": "Read dataset from csv file", "topics": [ "Read" ] }, { "page": "ReadExtResult", "title": "Read results from other methods", "topics": [ "ReadExtResult" ] }, { "page": "readHeader", "title": "Read the header of the dataset", "topics": [ "readHeader" ] }, { "page": "Spearman", "title": "miRNA target prediction with the Spearman correlation coefficient method", "topics": [ "Spearman" ] }, { "page": "Standardise", "title": "Stardarsise the dataset Stadardise the dataset to have mean=0 and std=1 in each column.", "topics": [ "Standardise" ] }, { "page": "ValidateAll", "title": "Validate the targets of all miRNA using both experimentally confirmed and transfection data", "topics": [ "ValidateAll" ] }, { "page": "Validation", "title": "Validate the targets of a miRNA", "topics": [ "Validation" ] }, { "page": "ValidationT", "title": "Validate the targets of a miRNA using transfection data", "topics": [ "ValidationT" ] }, { "page": "Zscore", "title": "miRNA target prediction with the Z-score method", "topics": [ "Zscore" ] } ], "_rundeps": [ "abind", "amap", "annotate", "AnnotationDbi", "AnnotationForge", "askpass", "backports", "base64enc", "bdsmatrix", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocManager", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "boot", "bslib", "cachem", "Category", "caTools", "checkmate", "cli", "clipr", "clue", "cluster", "codetools", "colorspace", "corpcor", "cpp11", "crayon", "ctc", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DEoptimR", "digest", "downloader", "dplyr", "energy", "entropy", "evaluate", "farver", "fastICA", "fastmap", "filelock", "fontawesome", "foreach", "foreign", "Formula", "fs", "genefilter", "generics", "GenomicRanges", "ggm", "ggplot2", "glmnet", "glue", "GO.db", "GOstats", "gplots", "graph", "gridExtra", "GSEABase", "gsl", "gtable", "gtools", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "impute", "inum", "InvariantCausalPrediction", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lattice", "libcoin", "lifecycle", "limma", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mboost", "memoise", "mime", "mvtnorm", "nnet", "nnls", "openssl", "org.Hs.eg.db", "partykit", "pcalg", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "purrr", "quadprog", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RBGL", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "readr", "Rgraphviz", "rlang", "rmarkdown", "robustbase", "rpart", "RSQLite", "rstudioapi", "rvest", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "selectr", "Seqinfo", "sfsmisc", "shape", "SparseArray", "stabs", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "TCGAbiolinks", "TCGAbiolinksGUI.data", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "vcd", "vctrs", "viridisLite", "vroom", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "miRLAB-vignette.Rmd", "filename": "miRLAB-vignette.html", "title": "miRLAB", "author": "Thuc Duy Le", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Conclusions", "References" ], "created": "2015-07-16 19:09:19", "modified": "2021-10-07 03:23:53", "commits": 2 } ], "_score": 4.681241237375588, "_indexed": false, "_nocasepkg": "mirlab", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/miRLAB", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.42.0", "date": "2026-05-29T07:27:41.000Z", "distro": "noble", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "615457c7c52a74a97965f214230f6be5868052a89343d24bb9b27c774a3bf6e9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.6.0", "os": "linux", "version": "1.42.0", "date": "2026-05-29T07:28:00.000Z", "distro": "noble", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "e2e677ee3b13d41eb108ecb8de2e37e00f55b444a5afae96aacaae0baedeadcb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.5.3", "os": "mac", "version": "1.42.0", "date": "2026-05-29T08:28:28.000Z", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "4b77bd17e08e39e264c56739a8ed2ee60268c86667f2ffb4a124946f82f49561", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.6.0", "os": "mac", "version": "1.42.0", "date": "2026-05-29T08:28:27.000Z", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "6fc3b374bae0bebea0c7473aab1069f196ae3424e6fe73b2920ff5568fbcecef", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.6.0", "os": "wasm", "version": "1.42.0", "date": "2026-05-29T07:27:48.000Z", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "adf82a4348b344d5fc815c9563231b34c89e5f5e2266ee13d524a87aed639d7c", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.7.0", "os": "win", "version": "1.42.0", "date": "2026-05-29T07:26:17.000Z", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "f89a83dfeff95bcb28cec5ac2fc0a6d873197d0cf02d8468d13e527056b958b2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.5.3", "os": "win", "version": "1.42.0", "date": "2026-05-29T07:25:39.000Z", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "4110e1e25be358ab448a51aede8873879c64b6861bbf556235699e1409f6b854", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" }, { "r": "4.6.0", "os": "win", "version": "1.42.0", "date": "2026-05-29T07:25:42.000Z", "commit": "2c560f8442f6ca1a3f20b9ac3d5cb81f65d4ad2f", "fileid": "d80a1a9752360678184ed25cf1a98578f219b55947f112f0d5d3fedaa5e8b85a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623825585" } ] }