{ "_id": "6a196808acfb0bcc41de844b", "Package": "BiSeq", "Type": "Package", "Title": "Processing and analyzing bisulfite sequencing data", "Version": "1.53.0", "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": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:37:40 UTC", "RemoteUrl": "https://github.com/bioc/BiSeq", "RemoteRef": "HEAD", "RemoteSha": "773a1eaf9f126a5919cd27316c3d9a03cdb70516", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:32:23 UTC", "User": "root" }, "MD5sum": "ddef9cfd210d15bb4be0ee79e30a8eff", "_user": "bioc", "_type": "src", "_file": "BiSeq_1.53.0.tar.gz", "_fileid": "17d63e1400ec07eef3a790157e4d6d58f5252f25ad4b7050e087eb6f65188d25", "_filesize": 1214758, "_sha256": "17d63e1400ec07eef3a790157e4d6d58f5252f25ad4b7050e087eb6f65188d25", "_created": "2026-05-29T08:32:23.000Z", "_published": "2026-05-29T10:18:48.795Z", "_jobs": [ { "job": 78466263653, "time": 197, 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"compareTwoSamples", "covBoxplots", "covStatistics", "estLocCor", "filterByCov", "filterBySharedRegions", "findDMRs", "globalTest", "limitCov", "logisticRegression", "makeVariogram", "methLevel", "methLevel<-", "methReads", "methReads<-", "plotBindingSites", "plotMeth", "plotMethMap", "plotSmoothMeth", "predictMeth", "rawToRel", "readBismark", "smoothVariogram", "summarizeRegions", "testClusters", "totalReads", "totalReads<-", "trimClusters", "writeBED" ], "_datasets": [ { "name": "betaResults", "title": "The output of 'betaRegression'", "object": "betaResults", "file": "betaResults.RData", "class": [ "data.frame" ], "fields": [ "chr", "pos", "p.val", "meth.group1", "meth.group2", "meth.diff", "estimate", "std.error", "pseudo.R.sqrt", "cluster.id" ], "rows": 344, "table": true, "tojson": true }, { "name": "betaResultsNull", "title": "The output of 'betaRegression' for resampled data", "object": "betaResultsNull", "file": "betaResultsNull.RData", "class": [ "data.frame" ], "fields": [ "chr", "pos", "p.val", "meth.group1", "meth.group2", "meth.diff", "estimate", "std.error", "pseudo.R.sqrt", "cluster.id" ], "rows": 344, "table": true, "tojson": true }, { "name": "DMRs", "title": "The output of 'findDMRs'", "object": "DMRs", "file": "DMRs.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "predictedMeth", "title": "The output of 'predictMeth'", "object": "predictedMeth", "file": "predictedMeth.RData", "class": [ "BSrel" ], "fields": [], "table": false, "tojson": false }, { "name": "promoters", "title": "A 'GRanges' of promoters of the human genome", "object": "promoters", "file": "promoters.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "rrbs", "title": "RRBS data of APL patient samples and controls.", "object": "rrbs", "file": "rrbs.RData", "class": [ "BSraw" ], "fields": [], "table": false, "tojson": false }, { "name": "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 variogram", "topics": [ "smoothVariogram", "smoothVariogram,list,numeric,missing-method", "smoothVariogram,list,numeric,numeric-method", "smoothVariogram,matrix,numeric,missing-method", "smoothVariogram,matrix,numeric,numeric-method" ] }, { "page": "summarizeRegions", "title": "Aggregates methylation information of single CpG sites", "topics": [ "summarizeRegions", "summarizeRegions,BSraw,GRanges,logical-method", "summarizeRegions,BSraw,GRanges,missing-method", "summarizeRegions,BSrel,GRanges,logical-method", "summarizeRegions,BSrel,GRanges,missing-method" ] }, { "page": "testClusters", "title": "Tests CpG clusters", "topics": [ "testClusters", "testClusters,list,missing-method", "testClusters,list,numeric-method" ] }, { "page": "trimClusters", "title": "Trims CpG clusters", "topics": [ "trimClusters", "trimClusters,list,missing-method", "trimClusters,list,numeric-method" ] }, { "page": "vario", "title": "Output of 'makeVariogram'", "topics": [ "vario" ] }, { "page": "writeBED", "title": "Writes 'BSraw' and 'BSrel' data to a bed file suitable for the IGV", "topics": [ "writeBED", 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