{ "_id": "6aafcb7a3d719c1f840822f3", "Package": "BiSeq", "Type": "Package", "Title": "Processing and analyzing bisulfite sequencing data", "Version": "1.52.0", "Date": "2025-07-24", "Author": "Katja Hebestreit, Hans-Ulrich Klein", "Maintainer": "Katja Hebestreit ", "Description": "The BiSeq package provides useful classes and functions to\nhandle and analyze targeted bisulfite sequencing (BS) data such\nas reduced-representation bisulfite sequencing (RRBS) data. In\nparticular, it implements an algorithm to detect differentially\nmethylated regions (DMRs). The package takes already aligned BS\ndata from one or multiple samples.", "License": "LGPL-3", "biocViews": "Genetics, Sequencing, MethylSeq, DNAMethylation", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:37:40 UTC", "RemoteUrl": "https://github.com/bioc/BiSeq", "RemoteRef": "RELEASE_3_23", "RemoteSha": "120889eee5ee8a98c976faa6f1f604da6b143784", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-20 11:53:21 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "BiSeq_1.52.0.tar.gz", "_fileid": "https://r2.ropensci.org/4c65fcc84f82b973855aafcc2d80c4b542e7bd29f26b71a4867d3f6ea6b5b54e", "_filesize": 1215400, "_sha256": "4c65fcc84f82b973855aafcc2d80c4b542e7bd29f26b71a4867d3f6ea6b5b54e", "_expires": "2026-12-29T12:03:04.000Z", "_created": "2026-09-20T11:53:21.000Z", "_published": "2026-09-20T12:03:06.449Z", "_bioccheck": { "error": 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"vario", "title": "Output of 'makeVariogram'", "object": "vario", "file": "vario.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "annotateGRanges", "title": "Annotates a 'GRanges' object by means of a second 'GRanges' object", "topics": [ "annotateGRanges", "annotateGRanges,GRanges,GRanges,character,character-method", "annotateGRanges,GRanges,GRanges,character,integer-method", "annotateGRanges,GRanges,GRanges,character,missing-method" ] }, { "page": "betaRegression", "title": "A function to estimate and test a group factor within a beta regression", "topics": [ "betaRegression", "betaRegression,formula,character,BSrel,missing-method", "betaRegression,formula,character,BSrel,numeric-method" ] }, { "page": "betaResults", "title": "The output of 'betaRegression'", "topics": [ "betaResults" ] }, { "page": "betaResultsNull", "title": "The output of 'betaRegression' for resampled data", "topics": [ "betaResultsNull" ] }, { "page": "binomLikelihoodSmooth", "title": "Calculates local likelihood estimations for binomial random variables", "topics": [ "binomLikelihoodSmooth", "binomLikelihoodSmooth,ANY-method" ] }, { "page": "BSraw-class", "title": "Class to contain raw Bisulfite Sequencing (BiSeq) Data", "topics": [ "BSraw", "BSraw,matrix,matrix,GRanges-method", "BSraw-class", "combine,BSraw,BSraw-method", "methReads", "methReads,BSraw-method", "methReads<-", "methReads<-,BSraw,matrix-method", "totalReads", "totalReads,BSraw-method", "totalReads<-", "totalReads<-,BSraw,matrix-method" ] }, { "page": "BSrel-class", "title": "Class to contain Bisulfite Sequencing (BiSeq) Data", "topics": [ "BSrel", "BSrel,matrix,GRanges-method", "BSrel-class", "combine,BSrel,BSrel-method", "methLevel", "methLevel,BSrel-method", "methLevel<-", "methLevel<-,BSrel,matrix-method" ] }, { "page": "clusterSites", "title": "Assigns CpG cluster memberships on CpG sites within 'BSraw' objects", "topics": [ "clusterSites", "clusterSites,BSraw,ANY,numeric,missing,missing,missing-method", "clusterSites,BSraw,ANY,numeric,missing,numeric,missing-method", "clusterSites,BSraw,ANY,numeric,numeric,missing,missing-method", "clusterSites,BSraw,ANY,numeric,numeric,numeric,missing-method", "clusterSites,BSraw,ANY,numeric,numeric,numeric,numeric-method", "clusterSites,BSraw,missing,missing,missing,missing,missing-method", "clusterSites,BSraw,missing,numeric,numeric,numeric,missing-method", "clusterSites,BSraw,missing,numeric,numeric,numeric,numeric-method" ] }, { "page": "clusterSitesToGR", "title": "A function to obtain a 'GRanges' object of CpG clusters from 'BSraw' and 'BSrel' objects", "topics": [ "clusterSitesToGR", "clusterSitesToGR,BSraw-method", "clusterSitesToGR,BSrel-method" ] }, { "page": "compareTwoSamples", "title": "Detects DMRs by comparing two samples", "topics": [ "compareTwoSamples", "compareTwoSamples,BSraw,character,character,numeric,numeric-method", "compareTwoSamples,BSraw,numeric,numeric,numeric,numeric-method", "compareTwoSamples,BSrel,character,character,numeric,numeric-method", "compareTwoSamples,BSrel,numeric,numeric,numeric,numeric-method" ] }, { "page": "covBoxplots", "title": "Creates boxplots of coverages per sample", "topics": [ "covBoxplots", "covBoxplots,BSraw-method" ] }, { "page": "covStatistics", "title": "Prints a short summary of coverage statistics per sample", "topics": [ "covStatistics", "covStatistics,BSraw-method", "covStatistics,BSrel-method" ] }, { "page": "DMRs", "title": "The output of 'findDMRs'", "topics": [ "DMRs" ] }, { "page": "estLocCor", "title": "Estimates the correlations of the z-scores", "topics": [ "estLocCor", "estLocCor,list-method" ] }, { "page": "filterByCov", "title": "Filters regions (or single CpGs) of a 'BSraw' object with a minimum coverage", "topics": [ "filterByCov", "filterByCov,BSraw,missing,logical-method", "filterByCov,BSraw,missing,missing-method", "filterByCov,BSraw,numeric,logical-method", "filterByCov,BSraw,numeric,missing-method" ] }, { "page": "filterBySharedRegions", "title": "Reduces a 'BSraw' or 'BSrel' object to regions (or single CpGs) shared by a fraction of samples", "topics": [ "filterBySharedRegions", "filterBySharedRegions,BSraw,ANY,missing,numeric,missing-method", "filterBySharedRegions,BSraw,ANY,missing,numeric,numeric-method", "filterBySharedRegions,BSraw,ANY,numeric,missing,missing-method", "filterBySharedRegions,BSraw,ANY,numeric,missing,numeric-method", "filterBySharedRegions,BSraw,missing,missing,missing,missing-method", "filterBySharedRegions,BSraw,missing,missing,missing,numeric-method", "filterBySharedRegions,BSraw,missing,missing,numeric,missing-method", "filterBySharedRegions,BSraw,missing,missing,numeric,numeric-method", "filterBySharedRegions,BSraw,missing,numeric,missing,missing-method", "filterBySharedRegions,BSraw,missing,numeric,missing,numeric-method", "filterBySharedRegions,BSrel,ANY,missing,numeric,ANY-method", "filterBySharedRegions,BSrel,ANY,numeric,missing,ANY-method", "filterBySharedRegions,BSrel,missing,missing,missing,ANY-method", "filterBySharedRegions,BSrel,missing,missing,numeric,ANY-method", "filterBySharedRegions,BSrel,missing,numeric,missing,ANY-method" ] }, { "page": "findDMRs", "title": "Aggregates CpG sites to DMRs", "topics": [ "findDMRs", "findDMRs,data.frame,missing,numeric,logical-method", "findDMRs,data.frame,missing,numeric,missing-method", "findDMRs,data.frame,numeric,numeric,logical-method", "findDMRs,data.frame,numeric,numeric,missing-method" ] }, { "page": "globalTest", "title": "Test whether at least one CpG is differentially methylated in a given genomic region", "topics": [ "globalTest", "globalTest,ANY,BSrel-method" ] }, { "page": "limitCov", "title": "Limits the coverage of a 'BSraw' object", "topics": [ "limitCov", "limitCov,BSraw,numeric-method" ] }, { "page": "logisticRegression", "title": "Estimates and tests a group factor", "topics": [ "logisticRegression", "logisticRegression,formula,character,BSrel,missing-method", "logisticRegression,formula,character,BSrel,numeric-method" ] }, { "page": "makeVariogram", "title": "Variogram estimator.", "topics": [ "makeVariogram", "makeVariogram,data.frame,logical,missing,missing-method", "makeVariogram,data.frame,logical,missing,numeric-method", "makeVariogram,data.frame,logical,numeric,missing-method", "makeVariogram,data.frame,logical,numeric,numeric-method", "makeVariogram,data.frame,missing,missing,missing-method", "makeVariogram,data.frame,missing,numeric,numeric-method" ] }, { "page": "plotBindingSites", "title": "Plots the mean methylation of given regions", "topics": [ "plotBindingSites", "plotBindingSites,BSraw,GRanges-method", "plotBindingSites,BSrel,GRanges-method" ] }, { "page": "plotMeth", "title": "Plots raw and smoothed methylation data for a given region", "topics": [ "plotMeth", "plotMeth,BSraw,BSrel,GRanges-method" ] }, { "page": "plotMethMap", "title": "Plots methylation values of multiple samples in a given region", "topics": [ "plotMethMap", "plotMethMap,BSraw,GRanges,factor,logical-method", "plotMethMap,BSraw,GRanges,factor,missing-method", "plotMethMap,BSraw,GRanges,missing,logical-method", "plotMethMap,BSraw,GRanges,missing,missing-method", "plotMethMap,BSrel,GRanges,factor,logical-method", "plotMethMap,BSrel,GRanges,factor,missing-method", "plotMethMap,BSrel,GRanges,missing,logical-method", "plotMethMap,BSrel,GRanges,missing,missing-method" ] }, { "page": "plotSmoothMeth", "title": "Plots smoothed methylation values for a bunch of samples and a given region", "topics": [ "plotSmoothMeth", "plotSmoothMeth,BSrel,GRanges,ANY,logical-method", "plotSmoothMeth,BSrel,GRanges,ANY,missing-method" ] }, { "page": "predictedMeth", "title": "The output of 'predictMeth'", "topics": [ "predictedMeth" ] }, { "page": "predictMeth", "title": "Predicts methylation levels along CpG sites or for a grid of sites in CpG clusters.", "topics": [ "predictMeth", "predictMeth,BSraw,missing,missing,missing-method", "predictMeth,BSraw,missing,missing,numeric-method", "predictMeth,BSraw,numeric,missing,missing-method", "predictMeth,BSraw,numeric,missing,numeric-method", "predictMeth,BSraw,numeric,numeric,numeric-method" ] }, { "page": "promoters", "title": "A 'GRanges' of promoters of the human genome", "topics": [ "promoters" ] }, { "page": "rawToRel", "title": "Converts a 'BSraw' object to a 'BSrel' object", "topics": [ "rawToRel", "rawToRel,BSraw-method" ] }, { "page": "readBismark", "title": "Reads cytosine methylation stati determined by Bismark", "topics": [ "readBismark", "readBismark,character,character-method", "readBismark,character,data.frame-method", "readBismark,character,DataFrame-method" ] }, { "page": "rrbs", "title": "RRBS data of APL patient samples and controls.", "topics": [ "rrbs" ] }, { "page": "smoothVariogram", "title": "Smoothes 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