{ "_id": "6a196710acfb0bcc41de7aac", "Package": "BUScorrect", "Type": "Package", "Title": "Batch Effects Correction with Unknown Subtypes", "Version": "1.31.0", "Date": "2018-06-07", "Author": "Xiangyu Luo , Yingying Wei\n", "Maintainer": "Xiangyu Luo ", "Description": "High-throughput experimental data are accumulating\nexponentially in public databases. However, mining valid\nscientific discoveries from these abundant resources is\nhampered by technical artifacts and inherent biological\nheterogeneity. The former are usually termed \"batch effects,\"\nand the latter is often modelled by \"subtypes.\" The R package\nBUScorrect fits a Bayesian hierarchical model, the\nBatch-effects-correction-with-Unknown-Subtypes model (BUS), to\ncorrect batch effects in the presence of unknown subtypes. BUS\nis capable of (a) correcting batch effects explicitly, (b)\ngrouping samples that share similar characteristics into\nsubtypes, (c) identifying features that distinguish subtypes,\nand (d) enjoying a linear-order computation complexity.", "VignetteBuilder": "knitr", "biocViews": "GeneExpression, StatisticalMethod, Bayesian, Clustering,\nFeatureExtraction, BatchEffect", "LazyLoad": "yes", "License": "GPL (>= 2)", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:30 UTC", "RemoteUrl": "https://github.com/bioc/BUScorrect", "RemoteRef": "HEAD", "RemoteSha": "3213fae03e5deadb539a0a7334378a5a221889f0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 08:30:38 UTC", "User": "root" }, "MD5sum": "0d6854a19745233a6af89781d7431668", "_user": "bioc", "_type": "src", "_file": "BUScorrect_1.31.0.tar.gz", "_fileid": "7a536f20e1d2ac1facf82b11f95d7ddd8bb9770ad1035c4a02f6f10b1c60606d", "_filesize": 3840848, "_sha256": 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"https://github.com/r-universe/bioc/actions/runs/26626671446", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BUScorrect", "_commit": { "id": "3213fae03e5deadb539a0a7334378a5a221889f0", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380510 }, "_maintainer": { "name": "Xiangyu Luo", "email": "xyluo1991@gmail.com", "login": "xiangyuluo", "description": "\n Associate Professor (with tenure), Institute of Statistics and Big Data, Renmin University of China\n", "uuid": 25922838 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "gplots", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "statisticalmethod", "bayesian", "clustering", "featureextraction", "batcheffect" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 372, "source": "https://www.bioconductor.org/packages/stats/bioc/BUScorrect" }, "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/BUScorrect.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "adjusted_values", "baseline_expression_values", "BIC_BUS", "BUSgibbs", "calculate_EPSR_gamma", "calculate_EPSR_mu", "calculate_EPSR_sigma_sq", "estimate_IG_indicators", "IG_index", "location_batch_effects", "postprob_DE", "postprob_DE_thr_fun", "scale_batch_effects", "subtype_effects", "Subtypes", "visualize_data" ], "_datasets": [ { "name": "BUSexample_data", "title": "A simulated data set", "object": "BUSexample_data", "file": "BUSexample_data.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "BUScorrect-package", "title": "Batch Effects Correction with Unknown Subtypes", "topics": [ "BUScorrect-package", "BUScorrect" ] }, { "page": "adjusted_values", "title": "Obtain adjusted expression values from the output by BUSgibbs", "topics": [ "adjusted_values" ] }, { "page": "baseline_expression_values", "title": "Obtain the baseline expression values from the output by BUSgibbs", "topics": [ "baseline_expression_values" ] }, { "page": "BIC_BUS", "title": "Obtain BIC form the output by BUSgibbs", "topics": [ "BIC_BUS" ] }, { "page": "BUSexample_data", "title": "A simulated data set", "topics": [ "BUSexample_data" ] }, { "page": "BUSgibbs", "title": "Batch Effects Correction and Subtype Discovery using Gibbs Sampler", "topics": [ "BUSgibbs" ] }, { "page": "calculate_EPSR_gamma", "title": "Calculate the estimated potential scale reduction factors (EPSR factors) for location batch effects", "topics": [ "calculate_EPSR_gamma" ] }, { "page": "calculate_EPSR_mu", "title": "Calculate the estimated potential scale reduction factors (EPSR factors) for subtype effects", "topics": [ "calculate_EPSR_mu" ] }, { "page": "calculate_EPSR_sigma_sq", "title": "Calculate the estimated potential scale reduction factors (EPSR factors) for the variances of expression values", "topics": [ "calculate_EPSR_sigma_sq" ] }, { "page": "estimate_IG_indicators", "title": "Estimate the intrinsic gene indicators", "topics": [ "estimate_IG_indicators" ] }, { "page": "IG_index", "title": "Obtain the intrinsic gene indices", "topics": [ "IG_index" ] }, { "page": "location_batch_effects", "title": "Obtain the location batch effects from the output by BUSgibbs", "topics": [ "location_batch_effects" ] }, { "page": "postprob_DE", "title": "Calculate the posterior probability of being differentially expressed", "topics": [ "postprob_DE" ] }, { "page": "postprob_DE_thr_fun", "title": "Select the the posterior probability threshold to control the false discovery rate", "topics": [ "postprob_DE_thr_fun" ] }, { "page": "print.BUSfits", "title": "Print the output by BUSgibbs", "topics": [ "print.BUSfits" ] }, { "page": "scale_batch_effects", "title": "Obtain the scale batch effects from the output by 'BUSgibbs'", "topics": [ "scale_batch_effects" ] }, { "page": "subtype_effects", "title": "Obtain the subtype effects from the output by 'BUSgibbs'", "topics": [ "subtype_effects" ] }, { "page": "Subtypes", "title": "Obtain the subtype indicators from the output by 'BUSgibbs'", "topics": [ "Subtypes" ] }, { "page": "summary.BUSfits", "title": "Summary the output by 'BUSgibbs'", "topics": [ "summary.BUSfits" ] }, { "page": "visualize_data", "title": "Visualize the gene expression data from multiple batches", "topics": [ "visualize_data" ] } ], "_readme": "https://github.com/bioc/BUScorrect/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "bitops", "caTools", "DelayedArray", "generics", "GenomicRanges", "gplots", "gtools", "IRanges", "KernSmooth", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "BUScorrect_user_guide.Rnw", "filename": "BUScorrect_user_guide.pdf", "title": "BUScorrect_user_guide", "engine": "knitr::knitr", "headings": [], "created": "2018-06-26 12:19:42", "modified": "2018-07-23 03:45:06", "commits": 4 } ], "_score": 4, "_indexed": true, "_nocasepkg": "buscorrect", "_universes": [ "bioc", "xiangyuluo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-05-29T08:33:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "3213fae03e5deadb539a0a7334378a5a221889f0", "fileid": "e664d9e74cce9ccb07c7ea5426608586cf3527642b1b8b27a9f5e23276f7956d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626671446" }, { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-05-29T08:33:21.000Z", "distro": "noble", "arch": "x86_64", "commit": "3213fae03e5deadb539a0a7334378a5a221889f0", "fileid": "36bcb51ac5baf0bd1d1dd1bfcc449cb3bb8abb9295a43bb3870db762f7f8b86b", "status": "success", "check": "NOTE", "buildurl": 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