{ "_id": "6a1a74481d7bb097a09d156a", "Package": "mirTarRnaSeq", "Type": "Package", "Title": "mirTarRnaSeq", "Version": "1.21.0", "Authors@R": "c(person(given = \"Mercedeh\",\nfamily = \"Movassagh\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mercedeh@ds.dfci.harvard.edu\",\ncomment = c(ORCID = \"0000-0001-7690-0230\")),\nperson(\"Sarah\",\"Morton\", role=\"aut\"),\nperson(\"Rafael\",\"Irizarry\", role=\"aut\"),\nperson(\"Jeffrey\", \"Bailey\", role= \"aut\"),\nperson(\"Joseph N\", \"Paulson\", email=\"paulson.joseph@gene.com\", role=\"aut\"))", "Description": "mirTarRnaSeq R package can be used for interactive mRNA\nmiRNA sequencing statistical analysis. This package utilizes\nexpression or differential expression mRNA and miRNA sequencing\nresults and performs interactive correlation and various GLMs\n(Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis\nbetween mRNA and miRNA expriments. These experiments can be\ntime point experiments, and or condition expriments.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "DeploySubPath": "mirTarRnaSeq", "biocViews": "miRNA, Regression, Software, Sequencing, SmallRNA,\nTimeCourse, DifferentialExpression", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:34 UTC", "RemoteUrl": "https://github.com/bioc/mirTarRnaSeq", "RemoteRef": "HEAD", "RemoteSha": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 09:28:11 UTC", "User": "root" }, "Author": "Mercedeh Movassagh [aut, cre] (ORCID:\n),\nSarah Morton [aut],\nRafael Irizarry [aut],\nJeffrey Bailey [aut],\nJoseph N Paulson [aut]", "Maintainer": "Mercedeh Movassagh ", "MD5sum": "6f87c13b1ab2b589a01b72643b2ff21b", "_user": "bioc", "_type": "src", "_file": "mirTarRnaSeq_1.21.0.tar.gz", "_fileid": "63c76c12dacf77de3d9d115cbee08578a697e714360f2fa00f17c3f307731f3f", "_filesize": 6820707, "_sha256": "63c76c12dacf77de3d9d115cbee08578a697e714360f2fa00f17c3f307731f3f", "_created": "2026-05-29T09:28:11.000Z", "_published": "2026-05-30T05:23:20.632Z", "_jobs": [ { "job": 78626319266, "time": 200, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7305648630" }, { "job": 78626319366, "time": 278, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7287601160" }, { "job": 78626319453, "time": 259, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7287595248" }, { "job": 78626319510, "time": 144, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7289336195" }, { "job": 78626319472, "time": 94, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7289306437" }, { "job": 78626319242, "time": 412, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7287512513" }, { "job": 78626319375, "time": 167, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7287566574" }, { "job": 78626319322, "time": 152, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7305641998" }, { "job": 78626319461, "time": 141, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7287558026" }, { "job": 78626319397, "time": 137, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7287557045" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/mirTarRnaSeq", "_commit": { "id": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380934 }, "_maintainer": { "name": "Mercedeh Movassagh", "email": "mercedeh@ds.dfci.harvard.edu", "login": "mercedeh66", "description": "", "uuid": 22622865, "orcid": "0000-0001-7690-0230" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "purrr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "pscl", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "caTools", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "corrplot", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "R.cache", "role": "Suggests" }, { "package": "SPONGE", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "mirna", "regression", "software", "sequencing", "smallrna", "timecourse", "differentialexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 362, "source": "https://www.bioconductor.org/packages/stats/bioc/mirTarRnaSeq" }, "_searchresults": 16, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mirTarRnaSeq.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "combiner", "corMirnaRna", "corMirnaRnaMiranda", "drawCorPlot", "drawInterPlots", "fdrSig", "finInterResult", "geneVari", "getInputSpecies", "glm_gaussian", "glm_multi", "glm_nb", "glm_poisson", "glm_zeroinfl", "glm_zeroinfl_negbin", "glm_zeroinfl_poisson", "miRanComp", "miranda_sponge_predict", "miRandaIntersect", "mirandaIntersectInter", "mirRnaDensityCor", "mirRnaDensityInter", "mirRnaHeatmap", "mirRnaHeatmapDiff", "modelAIC", "modelCoefficients", "modelData", "modelModelName", "modelModelPvalue", "modelsFilter", "modelTermPvalues", "one2manySponge", "one2OneRnaMiRNA", "plotFit", "plotResiduals", "plotTerms", "runAllMirnaModels", "runModel", "runModels", "sampCorRnaMirna", "threshSig", "threshSigInter", "twoTimePoint", "twoTimePointSamp", "tzTrans" ], "_datasets": [ { "name": "Combine", "title": "This is data is the mRNA expression across samples and miRNA expression data which is to be investigated in one file. This data set is used in documentation examples.", "object": "Combine", "class": [ "data.frame" ], "fields": [ "A73", "BALF1", "BALF2", "BALF3", "BALF4", "BALF5", "BARF0", "BaRF1", "BARF1", "BBLF1", "BBLF2/BBLF3", "BBLF4", "BBRF1", "BBRF2", "BBRF3", "BcLF1", "BcRF1", "BCRF1", "BDLF1", "BDLF2", "BDLF3", "BDLF3.5", "BDLF4", "BdRF1", "BFLF1", "BFLF2", "BFRF1", "BFRF1A", "BFRF2", "BFRF3", "BGLF1", "BGLF2", "BGLF3", "BGLF3.5", "BGLF4", "BGLF5", "BGRF1/BDRF1", "BHLF1", "BHRF1", "BILF1", "BILF2", "BKRF2", "BKRF3", "BKRF4", "BLLF1", "BLLF2", "BLLF3", "BLRF1", "BLRF2", "BMRF1", "BMRF2", "BNLF2a", "BNLF2b", "BNRF1", "BOLF1", "BORF1", "BORF2", "BPLF1", "BRLF1", "BRRF1", "BRRF2", "BSLF1", "BSLF2/BMLF1", "BSRF1", "BTRF1", "BVLF1", "BVRF1", "BVRF2", "BWRF1", "BXLF1", "BXLF2", "BXRF1", "BZLF1", "BZLF2", "Cp", "DS", "EBER1", "EBER2", "EBNA-1", "EBNA-2", "EBNA-3A", "EBNA-3B", "EBNA-3C", "EBNA-LP", "LF1", "LF2", "LF3", "LMP-1", "LMP-2A", "LMP-2B", "oriLyt", "oriP", "RPMS1", "TR", "Wp", "Zp", "ebv-mir-bart9-5p" ], "rows": 25, "table": true, "tojson": true }, { "name": "corr_0", "title": "This is data is the mRNA FC and miRNA FC correlation data. This data set is used in documentation examples.", "object": "corr_0", "class": [ "data.frame" ], "fields": [ "V1", "V2", "value" ], "rows": 49776, "table": true, "tojson": true }, { "name": "final_results", "title": "This is data is the mRNA FC and miRNA FC correlation/interaction data results after filteration. This data set is used in documentation examples.", "object": "final_results", "class": [ "data.frame" ], "fields": [ "mRNA", "miRNA", "FC_mRNA", "FC_miRNA", "pvalue" ], "rows": 9, "table": true, "tojson": true }, { "name": "geneVariant", "title": "This is data is the mRNA expression across samples and miRNA expression data which is to be investigated giving directions on which data is miRNA and which is mRNA. This data set is used in documentation examples.", "object": "geneVariant", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "inter0", "title": "This is data is the mRNA FC and miRNA FC correlation/interaction original data. This data set is used in documentation examples.", "object": "inter0", "class": [ "data.frame" ], "fields": [ "V1", "V2", "value" ], "rows": 49776, "table": true, "tojson": true }, { "name": "miRanda", "title": "This is data is the results file from EBV miRanda getInputSpecies function. This data set is used in documentation examples.", "object": "miRanda", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6" ], "rows": 61893, "table": true, "tojson": true }, { "name": "miRandaM", "title": "This is data is the results file from mouse miRanda getInputSpecies function. This data set is used in documentation examples.", "object": "miRandaM", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6" ], "rows": 92062, "table": true, "tojson": true }, { "name": "miRNA", "title": "This is data is the miRNA expression file. This data set is used in documentation examples.", "object": "miRNA", "class": [ "data.frame" ], "fields": [ "Stom_363", "Stom_072", "Stom_424", "Stom_325", "Stom_415", "Stom_307", "Stom_156", "Stom_137", "Stom_211", "Stom_095", "Stom_286", "Stom_362", "Stom_326", "Stom_350", "Stom_315", "Stom_087", "Stom_163", "Stom_221", "Stom_301", "Stom_361", "Stom_073", "Stom_069", "Stom_109", "Stom_406", "Stom_394", "Stom_336" ], "rows": 40, "table": true, "tojson": true }, { "name": "miRNA_fc", "title": "This is data is the combined miRNA FC for all time points. This data set is used in documentation examples.", "object": "miRNA_fc", "class": [ "data.frame" ], "fields": [ "FC1", "FC2", "FC3" ], "rows": 408, "table": true, "tojson": true }, { "name": "miRNA_fc2", "title": "This data is the miRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.", "object": "miRNA_fc2", "class": [ "data.frame" ], "fields": [ "FC1" ], "rows": 408, "table": true, "tojson": true }, { "name": "miRNA0_2", "title": "This is data is the miRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.", "object": "miRNA0_2", "class": [ "data.frame" ], "fields": [ "Gene", "FC" ], "rows": 408, "table": true, "tojson": true }, { "name": "miRNA0_5", "title": "This is data is the miRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.", "object": "miRNA0_5", "class": [ "data.frame" ], "fields": [ "Gene", "FC" ], "rows": 408, "table": true, "tojson": true }, { "name": "miRNA2_5", "title": "This is data is the miRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.", "object": "miRNA2_5", "class": [ "data.frame" ], "fields": [ "Gene", "FC" ], "rows": 408, "table": true, "tojson": true }, { "name": "mRNA", "title": "This is data is the mRNA expression file. This data set is used in documentation examples.", "object": "mRNA", "class": [ "data.frame" ], "fields": [ "Stom_069", "Stom_072", "Stom_073", "Stom_087", "Stom_095", "Stom_109", "Stom_137", "Stom_156", "Stom_163", "Stom_221", "Stom_286", "Stom_301", "Stom_307", "Stom_315", "Stom_325", "Stom_326", "Stom_336", "Stom_350", "Stom_361", "Stom_362", "Stom_363", "Stom_394", "Stom_406", "Stom_415", "Stom_424" ], "rows": 96, "table": true, "tojson": true }, { "name": "mRNA_fc", "title": "This is data is the combined mRNA FC for all time points. This data set is used in documentation examples.", "object": "mRNA_fc", "class": [ "data.frame" ], "fields": [ "FC1", "FC2", "FC3" ], "rows": 122, "table": true, "tojson": true }, { "name": "mRNA_fc2", "title": "This data is the mRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.", "object": "mRNA_fc2", "class": [ "data.frame" ], "fields": [ "FC1" ], "rows": 122, "table": true, "tojson": true }, { "name": "mRNA0_2", "title": "This is data is the mRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.", "object": "mRNA0_2", "class": [ "data.frame" ], "fields": [ "Gene", "FC", "pvalue" ], "rows": 22658, "table": true, "tojson": true }, { "name": "mRNA0_5", "title": "This is data is the mRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.", "object": "mRNA0_5", "class": [ "data.frame" ], "fields": [ "Gene", "FC", "pvalue" ], "rows": 22634, "table": true, "tojson": true }, { "name": "mRNA2_5", "title": "This is data is the mRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.", "object": "mRNA2_5", "class": [ "data.frame" ], "fields": [ "Gene", "FC", "pvalue" ], "rows": 22834, "table": true, "tojson": true }, { "name": "outs", "title": "This is data is the output file resulted from time point/conditions background correlation model. This data set is used in documentation examples.", "object": "outs", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "outs2", "title": "This is data is the output file resulted from time point/conditions background difference/interelation model. This data set is used in documentation examples.", "object": "outs2", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "results", "title": "This is data is the output file resulted from time point or conditions or correlation or interrelation model. This data set is used in documentation examples.", "object": "results", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "sig_corrs", "title": "This is data is the output file resulted from time point or conditions experiment for correlation model after filtering and threshold modification. This data set is used in documentation examples.", "object": "sig_corrs", "class": [ "data.frame" ], "fields": [ "V1", "V2", "value" ], "rows": 8212, "table": true, "tojson": true }, { "name": "sig_InterR", "title": "This is data is the output file resulted from time point or conditions experiment for interrelation model after filtering and threshold modification. This data set is used in documentation examples.", "object": "sig_InterR", "class": [ "data.frame" ], "fields": [ "V1", "V2", "value" ], "rows": 2484, "table": true, "tojson": true }, { "name": "some_model", "title": "This is data is the results file from regression analysis and its estimates. This data set is used in documentation examples.", "object": "some_model", "class": [ "glm", "lm" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "canonicalModel_", "title": "Decifer a 'model parameter' and run appropriate 'glm_...' function.", "topics": [ "canonicalModel_" ] }, { "page": "Combine", "title": "This is data is the mRNA expression across samples and miRNA expression data which is to be investigated in one file. This data set is used in documentation examples.", "topics": [ "Combine" ] }, { "page": "combiner", "title": "combiner combines the miRNA and mRNA files", "topics": [ "combiner" ] }, { "page": "corMirnaRna", "title": "corMirnaRna correlation for miRNA and mRNA", "topics": [ "corMirnaRna" ] }, { "page": "corMirnaRnaMiranda", "title": "corMirnaRnaMiranda correlation for miRNA and mRNA", "topics": [ "corMirnaRnaMiranda" ] }, { "page": "corr_0", "title": "This is data is the mRNA FC and miRNA FC correlation data. This data set is used in documentation examples.", "topics": [ "corr_0" ] }, { "page": "downloadMirandaFile", "title": "downloadMirandaFile Read internal Miranda file", "topics": [ "downloadMirandaFile" ] }, { "page": "drawCorPlot", "title": "drawCorPlot correlation plots for mRNA and miRNA regression results", "topics": [ "drawCorPlot" ] }, { "page": "drawInterPlots", "title": "drawInterPlots for finInterResult miRNA and mRNA Interrelation real data", "topics": [ "drawInterPlots" ] }, { "page": "fdrSig", "title": "fdrSig Ruturns FDR significant miRNA/mRNA predictions", "topics": [ "fdrSig" ] }, { "page": "final_results", "title": "This is data is the mRNA FC and miRNA FC correlation/interaction data results after filteration. This data set is used in documentation examples.", "topics": [ "final_results" ] }, { "page": "finInterResult", "title": "finInterResult miRNA and mRNA interrelation in two-time points results in a dataframe.", "topics": [ "finInterResult" ] }, { "page": "geneVari", "title": "geneVari Makes a list of gene names to be used in the runModels function", "topics": [ "geneVari" ] }, { "page": "geneVariant", "title": "This is data is the mRNA expression across samples and miRNA expression data which is to be investigated giving directions on which data is miRNA and which is mRNA. This data set is used in documentation examples.", "topics": [ "geneVariant" ] }, { "page": "getInputSpecies", "title": "Return Miranda data for a given species.", "topics": [ "getInputSpecies" ] }, { "page": "glm_gaussian", "title": "Model functions for GLM with Gaussian model.", "topics": [ "glm_gaussian" ] }, { "page": "glm_multi", "title": "Model functions for GLM with negative binomial family.", "topics": [ "glm_multi" ] }, { "page": "glm_nb", "title": "Model functions for GLM with negative binomial family.", "topics": [ "glm_nb" ] }, { "page": "glm_poisson", "title": "Model functions for GLM with Poisson model.", "topics": [ "glm_poisson" ] }, { "page": "glm_zeroinfl", "title": "Model functions for zero inflated model using either Poisson or Negative Binomial distributions.", "topics": [ "glm_zeroinfl" ] }, { "page": "glm_zeroinfl_negbin", "title": "alias for glm_zeroinfl(\"negbin\")", "topics": [ "glm_zeroinfl_negbin" ] }, { "page": "glm_zeroinfl_poisson", "title": "alias for glm_zeroinfl(\"poisson\")", "topics": [ "glm_zeroinfl_poisson" ] }, { "page": "importMirandaFile", "title": "importMirandaFile Read internal Miranda file", "topics": [ "importMirandaFile" ] }, { "page": "inter0", "title": "This is data is the mRNA FC and miRNA FC correlation/interaction original data. This data set is used in documentation examples.", "topics": [ "inter0" ] }, { "page": "makeFormulaRightSide", "title": "makeFormulaRightSide makes right hand side of formula for model variables: vector of indep. variables", "topics": [ "makeFormulaRightSide" ] }, { "page": "miRanComp", "title": "miRanComp comparison of mRNAs present with miRanda file targets", "topics": [ "miRanComp" ] }, { "page": "miRanda", "title": "This is data is the results file from EBV miRanda getInputSpecies function. This data set is used in documentation examples.", "topics": [ "miRanda" ] }, { "page": "miranda_sponge_predict", "title": "Transform miRanda data for relevant mRNA and miRNA to matrix form compatible with sponge", "topics": [ "miranda_sponge_predict" ] }, { "page": "miRandaIntersect", "title": "miRandaIntersect Looks for Intersection of Significant output results with miRanda Results from getInputSpeciesDF function", "topics": [ "miRandaIntersect" ] }, { "page": "mirandaIntersectInter", "title": "mirandaIntersectInter Looks for Intersection of Significant output results with miRanda Results from getInputSpeciesDF function", "topics": [ "mirandaIntersectInter" ] }, { "page": "miRandaM", "title": "This is data is the results file from mouse miRanda getInputSpecies function. This data set is used in documentation examples.", "topics": [ "miRandaM" ] }, { "page": "miRNA", "title": "This is data is the miRNA expression file. This data set is used in documentation examples.", "topics": [ "miRNA" ] }, { "page": "miRNA_fc", "title": "This is data is the combined miRNA FC for all time points. This data set is used in documentation examples.", "topics": [ "miRNA_fc" ] }, { "page": "miRNA_fc2", "title": "This data is the miRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.", "topics": [ "miRNA_fc2" ] }, { "page": "miRNA0_2", "title": "This is data is the miRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.", "topics": [ "miRNA0_2" ] }, { "page": "miRNA0_5", "title": "This is data is the miRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.", "topics": [ "miRNA0_5" ] }, { "page": "miRNA2_5", "title": "This is data is the miRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.", "topics": [ "miRNA2_5" ] }, { "page": "mirRnaDensityCor", "title": "mirRnaDensityCor for miRTarRNASeq miRNA and mRNA correlation real data versus sampled data", "topics": [ "mirRnaDensityCor" ] }, { "page": "mirRnaDensityInter", "title": "mirRnaDensityInter for mirTarRnaSeq miRNA and mRNA Interrelation real data versus sampled data", "topics": [ "mirRnaDensityInter" ] }, { "page": "mirRnaHeatmap", "title": "mirRnaHeatmap pheatmap for miRTarRNASeq miRNA and mRNA correlation", "topics": [ "mirRnaHeatmap" ] }, { "page": "mirRnaHeatmapDiff", "title": "mirRnaHeatmapDiff heatmap for miRTarRNASeq miRNA and mRNA correlation", "topics": [ "mirRnaHeatmapDiff" ] }, { "page": "modelAIC", "title": "Obtain model AIC", "topics": [ "modelAIC" ] }, { "page": "modelCoefficients", "title": "Obtain coefficients", "topics": [ "modelCoefficients" ] }, { "page": "modelData", "title": "Obtain model input data", "topics": [ "modelData" ] }, { "page": "modelModelName", "title": "Obtain model name", "topics": [ "modelModelName" ] }, { "page": "modelModelPvalue", "title": "Obtain model p-value", "topics": [ "modelModelPvalue" ] }, { "page": "modelsFilter", "title": "modelsFilter Filter a list of models based on logical expression", "topics": [ "modelsFilter" ] }, { "page": "modelTermPvalues", "title": "Obtain p-values for terms in model formula", "topics": [ "modelTermPvalues" ] }, { "page": "mRNA", "title": "This is data is the mRNA expression file. This data set is used in documentation examples.", "topics": [ "mRNA" ] }, { "page": "mRNA_fc", "title": "This is data is the combined mRNA FC for all time points. This data set is used in documentation examples.", "topics": [ "mRNA_fc" ] }, { "page": "mRNA_fc2", "title": "This data is the mRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.", "topics": [ "mRNA_fc2" ] }, { "page": "mRNA0_2", "title": "This is data is the mRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.", "topics": [ "mRNA0_2" ] }, { "page": "mRNA0_5", "title": "This is data is the mRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.", "topics": [ "mRNA0_5" ] }, { "page": "mRNA2_5", "title": "This is data is the mRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.", "topics": [ "mRNA2_5" ] }, { "page": "one2manySponge", "title": "Sparse Partial Correlations On mRNA/miRNA Expression We make mirTarRnaSeq compatible to SPONGE package in order to estimate sparse matrix correlation (using elstic net) for prediction potential miRNA-mRNA interaction. Note this function/method is suggested for miRNA/mRNA interactions in many samples with a notable variance of mRNA/miRNA expression. This model also only reports negative sparse partial correlation predictions.", "topics": [ "one2manySponge" ] }, { "page": "one2OneRnaMiRNA", "title": "one2OneRnaMiRNA correlation for miRNA and mRNA using differntial expression fold change and if/when available p-value", "topics": [ "one2OneRnaMiRNA" ] }, { "page": "outs", "title": "This is data is the output file resulted from time point/conditions background correlation model. This data set is used in documentation examples.", "topics": [ "outs" ] }, { "page": "outs2", "title": "This is data is the output file resulted from time point/conditions background difference/interelation model. This data set is used in documentation examples.", "topics": [ "outs2" ] }, { "page": "plotFit", "title": "Plot model", "topics": [ "plotFit" ] }, { "page": "plotResiduals", "title": "Plot residuals", "topics": [ "plotResiduals" ] }, { "page": "plotTerms", "title": "plotTerms", "topics": [ "plotTerms" ] }, { "page": "results", "title": "This is data is the output file resulted from time point or conditions or correlation or interrelation model. This data set is used in documentation examples.", "topics": [ "results" ] }, { "page": "runAllMirnaModels", "title": "runAllMirnaModels runModel for all miRNAs", "topics": [ "runAllMirnaModels" ] }, { "page": "runModel", "title": "Run a model of a specific kind", "topics": [ "runModel" ] }, { "page": "runModels", "title": "runModels runs miRNA mrna model model for various miRNA-mRNA data distributions", "topics": [ "runModels" ] }, { "page": "sampCorRnaMirna", "title": "sampCorRnaMirna sampling for correlation for miRNA and mRNA", "topics": [ "sampCorRnaMirna" ] }, { "page": "sig_corrs", "title": "This is data is the output file resulted from time point or conditions experiment for correlation model after filtering and threshold modification. This data set is used in documentation examples.", "topics": [ "sig_corrs" ] }, { "page": "sig_InterR", "title": "This is data is the output file resulted from time point or conditions experiment for interrelation model after filtering and threshold modification. This data set is used in documentation examples.", "topics": [ "sig_InterR" ] }, { "page": "some_model", "title": "This is data is the results file from regression analysis and its estimates. This data set is used in documentation examples.", "topics": [ "some_model" ] }, { "page": "threshSig", "title": "threshSig Using shuffling threshold finds appropriate significant miRNA-mRNA correlation", "topics": [ "threshSig" ] }, { "page": "threshSigInter", "title": "threshSigInter Using shuffling threshold finds appropriate significant miRNA-mRNA correlation", "topics": [ "threshSigInter" ] }, { "page": "twoTimePoint", "title": "twoTimePoint miRNA and mRNA interrelation in two timepoints", "topics": [ "twoTimePoint" ] }, { "page": "twoTimePointSamp", "title": "twoTimePointSamp miRNA and mRNA interrelation in two timepoints sampling", "topics": [ "twoTimePointSamp" ] }, { "page": "tzTrans", "title": "tzTransTranspose and z-score transformation", "topics": [ "tzTrans" ] } ], "_pkglogo": "https://github.com/bioc/mirTarRnaSeq/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/mirTarRnaSeq/raw/HEAD/README.md", "_rundeps": [ "assertthat", "bitops", "caTools", "cli", "corrplot", "cpp11", "data.table", "dplyr", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "MASS", "pheatmap", "pillar", "pkgconfig", "plyr", "pscl", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "viridis", "viridisLite", "withr" ], "_vignettes": [ { "source": "mirTarRnaSeq.Rmd", "filename": "mirTarRnaSeq.html", "title": "mirTarRnaSeq", "author": "Mercedeh Movassagh", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data upload", "mirTarRnaSeq accepts data in dataframe or table formats", "Part1 - miRNA mRNA regressions across sample cohorts", "Uploading data into the application. The example data can be found in the test folder under package.", "Get miRanda file", "Select miRNA", "Combine the mRNA and miRNA file and define boundaries ans specify which mRNA and miRNA files in the combined file.", "Run a one to one miRNA/mRNA gaussian regression model (univariate model for 1 miRNA and 1 mRNA).", "Running Gaussian model over all individual miRNA mRNA models (univatiate model for every mRNA and miRNA relationship across the input dataset with Gaussian distribution assumptions)", "Running poisson model over all individual miRNA mRNA models (univatiate model for every mRNA and miRNA relationship across the input dataset with poisson distribution assumptions)", "Running negative binomial model over all individual miRNA mRNA models (univatiate model for every mRNA and miRNA relationship across the input dataset with negative bionomial distribution assumptions).", "Running zero inflated negative binomial model over all individual miRNA mRNA models (univatiate model for every mRNA and miRNA relationship across the input dataset with zero inflated negative bionomial distribution assumptions).", "Running zero inflated poisson binomial model over all individual miRNA mRNA models (univatiate model for every mRNA and miRNA relationship across the input dataset with zero inflated poisson distribution assumptions).", "Including Plots for all models to decide which to use", "The user can decide to use runModels() with glm_multi() (with multi and inter mode options)", "GLM multi and GLM inter", "Running all miRNA and mRNA combinations at the same time", "One2manySponge", "Part2 - Identify miRNA mRNA correlations across 3 or more time points", "Get mRNAs", "Get mRNAs with particular fold change", "Get all miRNAs", "Get mRNA miRNA correlation", "Make a background distribution correlation", "Plot density plots", "Get correlations below threshold", "Get mouse miRanda data", "mRNA miRNA correlation heatmap", "Get intersection of miRanda", "Part3 - Identify significant miRNA mRNA relationships for 2 time points", "Import data", "Only look for time point difference 0-5", "Get fold changes above thereshold", "Estimate miRNA mRNA differences based on Fold Change", "Make background distribution", "miRanda data import", "Identify relationships below threshold", "miRanda intersection with results", "Make dataframe and plots", "mRNA miRNA heatmap of miRNA mRNA FC differences" ], "created": "2021-02-23 02:11:16", "modified": "2022-04-06 23:19:17", "commits": 11 } ], "_score": 4.204119982655925, "_indexed": true, "_nocasepkg": "mirtarrnaseq", "_universes": [ "bioc", "mercedeh66" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-29T09:32:20.000Z", "distro": "noble", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "8af0d6898b156c9fbb4c2c9a2c4ac10056d514c9a98ac2debd88faed9325c945", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-29T09:32:10.000Z", "distro": "noble", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "6beeeeb695dba7bf48992b5f9ef2f1017f6444de6012adcff4b3d375f11a5adb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-29T11:13:07.000Z", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "f69f255e277b4639000ef6cc9412041058c4cef7605066c7c7957efe8f039713", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-29T11:11:31.000Z", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "52bca6e76bc275caf80c797d33d31e6da249325e9b6adf7c16c570a7e28a928b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-29T09:31:19.000Z", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "709d41b745af07a82e216cfa7dc8c51ec66d27e4fb0e4b0be803cd55845d435e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T05:20:11.000Z", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "a9925909504f27b71a842fefda5ea5ba0e6be96576a87fb70ca97bcf008e3d5b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-29T09:30:03.000Z", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "7214549b110fac96a2de56bad21f293ee6f17894e898159bbef17becac205707", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-29T09:30:00.000Z", "commit": "e1dbdc083cd388adfbd68c6f530d52737153aee6", "fileid": "aa53c62582dfbd5556b674cf735c70d209abaea08b6e771e2c0f6467772d7e8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26629179137" } ] }