{ "_id": "6a1050bfacfb0bcc41ca1239", "Package": "BICORN", "Title": "Integrative Inference of De Novo Cis-Regulatory Modules", "Version": "0.1.0", "Authors@R": "c(person(\"Xi\", \"Chen\", email = \"xichen86@vt.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Jianhua\", \"Xuan\", email = \"xuan@vt.edu\", role = \"aut\"))", "Description": "Prior transcription factor binding knowledge and target\ngene expression data are integrated in a Bayesian framework for\nfunctional cis-regulatory module inference. Using Gibbs\nsampling, we iteratively estimate transcription factor\nassociations for each gene, regulation strength for each\nbinding event and the hidden activity for each transcription\nfactor.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "6.0.1", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 05:25:14 UTC", "User": "root" }, "Author": "Xi Chen [aut, cre], Jianhua Xuan [aut]", "Maintainer": "Xi Chen ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2018-06-06 09:30:06 UTC", "RemoteUrl": "https://github.com/cran/BICORN", "RemoteRef": "HEAD", "RemoteSha": "acf2011f4a9491073cb2bd2d974626df4045e4f0", "MD5sum": "8edebd24e04c3001e8b3e86b3729be0d", "_user": "cran", "_type": "src", "_file": "BICORN_0.1.0.tar.gz", "_fileid": "24e11bc55e9cbc4be907def31725681034d09018104c535dddb4f493f7dfb023", "_filesize": 135009, "_sha256": "24e11bc55e9cbc4be907def31725681034d09018104c535dddb4f493f7dfb023", "_created": "2026-05-10T05:25:14.000Z", "_published": "2026-05-22T12:49:03.068Z", "_distro": "noble", "_jobs": [ { "job": 77382616576, "time": 108, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6901211693" }, { "job": 77382616736, "time": 121, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6901212949" }, { "job": 77382616271, "time": 159, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6901200209" }, { "job": 77382616324, "time": 92, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160856156" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/25620688935", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/BICORN", "_commit": { "id": "acf2011f4a9491073cb2bd2d974626df4045e4f0", "author": "Xi Chen ", "committer": "cran-robot ", "message": "version 0.1.0\n", "time": 1528277406 }, "_maintainer": { "name": "Xi Chen", "email": "xichen86@vt.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_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": 224, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BICORN" }, "_mentions": 2, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/BICORN.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2018-06-06" } ], "_exports": [ "BICORN", "data_integration" ], "_datasets": [ { "name": "Binding_genes", "title": "Genes in the prior binding network", "object": "sample.input", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Binding_matrix", "title": "Prior TF-gene binding network", "object": "sample.input", "class": [ "matrix", "array" ], "fields": [ "TF1", "TF2", "TF3", "TF4", "TF5", "TF6", "TF7", "TF8" ], "rows": 80, "table": true, "tojson": true }, { "name": "Binding_TFs", "title": "TFs in the prior binding network", "object": "sample.input", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Exp_data", "title": "Gene expression data", "object": "sample.input", "class": [ "matrix", "array" ], "fields": [ "Sample1", "Sample2", "Sample3", "Sample4", "Sample5", "Sample6", "Sample7", "Sample8", "Sample9", "Sample10", "Sample11", "Sample12" ], "rows": 80, "table": true, "tojson": true }, { "name": "Exp_genes", "title": "Genes in the expression data", "object": "sample.input", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "A", "title": "TF-gene regulation strength matrix", "topics": [ "A" ] }, { "page": "A_old", "title": "TF-gene regulation strength matrix sampled from the previous round", "topics": [ "A_old" ] }, { "page": "A_sampling", "title": "Regulation Strength Sampling Function", "topics": [ "A_sampling" ] }, { "page": "alpha", "title": "Inverse-gamma distribution hyper-parameter alpha", "topics": [ "alpha" ] }, { "page": "base_line", "title": "Gene baseline expression", "topics": [ "base_line" ] }, { "page": "base_line_old", "title": "Gene baseline expression sampled from the previous round.", "topics": [ "base_line_old" ] }, { "page": "baseline_sampling", "title": "Gene Baseline Expression Sampling Function", "topics": [ "baseline_sampling" ] }, { "page": "beta", "title": "Inverse-gamma distribution hyper-parameter beta", "topics": [ "beta" ] }, { "page": "BICORN", "title": "BICORN Algorithm Function", "topics": [ "BICORN" ] }, { "page": "Binding_genes", "title": "Genes in the prior binding network", "topics": [ "Binding_genes" ] }, { "page": "Binding_matrix", "title": "Prior TF-gene binding network", "topics": [ "Binding_matrix" ] }, { "page": "Binding_TFs", "title": "TFs in the prior binding network", "topics": [ "Binding_TFs" ] }, { "page": "C", "title": "TF-gene binding network", "topics": [ "C" ] }, { "page": "C_old", "title": "TF-gene binding network sampled from the previous round", "topics": [ "C_old" ] }, { "page": "C_prior", "title": "Prior TF-gene binding network", "topics": [ "C_prior" ] }, { "page": "C_sampling_cluster", "title": "cis-Regulatory Module Sampling Function", "topics": [ "C_sampling_cluster" ] }, { "page": "data_integration", "title": "Data Initialization for BICORN", "topics": [ "data_integration" ] }, { "page": "Exp_data", "title": "Gene expression data", "topics": [ "Exp_data" ] }, { "page": "Exp_genes", "title": "Genes in the expression data", "topics": [ "Exp_genes" ] }, { "page": "sigma_A", "title": "Regulation strength variance", "topics": [ "sigma_A" ] }, { "page": "sigma_baseline", "title": "Variance of baseline gene expression.", "topics": [ "sigma_baseline" ] }, { "page": "sigma_noise", "title": "Variance of gene expression fitting residuals.", "topics": [ "sigma_noise" ] }, { "page": "sigma_X", "title": "Transcription factor activity variance", "topics": [ "sigma_X" ] }, { "page": "sigmanoise_sampling", "title": "Fitting Residule Variance Sampling Function", "topics": [ "sigmanoise_sampling" ] }, { "page": "X", "title": "Transcription factr activity matrix", "topics": [ "X" ] }, { "page": "X_old", "title": "Transcription factr activity matrix sampled from the previous round", "topics": [ "X_old" ] }, { "page": "X_sampling", "title": "Transcription Factor Activity Sampling Function", "topics": [ "X_sampling" ] }, { "page": "Y", "title": "Gene expression data used for module inference", "topics": [ "Y" ] } ], "_rundeps": [], "_vignettes": [ { "source": "my-vignette.Rmd", "filename": "my-vignette.html", "title": "An Introduction to BICORN", "author": "Xi Chen", "engine": "knitr::rmarkdown", "headings": [ "Loading prior bindings and gene expression data", "Initializing BICORN", "Running BICORN", "BICORN outputs" ], "created": "2018-06-06 09:30:06", "modified": "2018-06-06 09:30:06", "commits": 1 } ], "_score": 2.3010299956639813, "_indexed": true, "_nocasepkg": "bicorn", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-05-10T05:27:05.000Z", "distro": "noble", "commit": "acf2011f4a9491073cb2bd2d974626df4045e4f0", "fileid": "1b2d793131f710505d79632257a0a29269d6160659bf76ed358f11b9de3a6273", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25620688935" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-05-10T05:27:18.000Z", "distro": "noble", "commit": "acf2011f4a9491073cb2bd2d974626df4045e4f0", "fileid": "b350d864a62f12f637f17ae1bd294695a9e21684fc6778f2958a0974743049cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25620688935" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-05-22T12:48:46.000Z", "commit": "acf2011f4a9491073cb2bd2d974626df4045e4f0", "fileid": "4509bf1b8f1007d7e08190ae4962520d7a97a74cea70e8f6c86f2e90593231ef", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25620688935" } ] }