{ "_id": "6a1acff01d7bb097a09e0eca", "Package": "genomation", "Type": "Package", "Title": "Summary, annotation and visualization of genomic data", "Version": "1.45.0", "Author": "Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna\nWreczycka [aut], Alexander Gosdschan [ctb], Liz Ing-Simmons\n[ctb], Bozena Mika-Gospodorz [ctb]", "Maintainer": "Altuna Akalin , Vedran Franke\n, Katarzyna Wreczycka\n", "Description": "A package for summary and annotation of genomic intervals.\nUsers can visualize and quantify genomic intervals over\npre-defined functional regions, such as promoters, exons,\nintrons, etc. The genomic intervals represent regions with a\ndefined chromosome position, which may be associated with a\nscore, such as aligned reads from HT-seq experiments, TF\nbinding sites, methylation scores, etc. The package can use any\ntabular genomic feature data as long as it has minimal\ninformation on the locations of genomic intervals. In addition,\nIt can use BAM or BigWig files as input.", "License": "Artistic-2.0", "LazyLoad": "yes", "VignetteBuilder": "knitr", "biocViews": "Annotation, Sequencing, Visualization, CpGIsland", "Encoding": "latin1", "URL": "http://bioinformatics.mdc-berlin.de/genomation/", "BugReports": "https://github.com/BIMSBbioinfo/genomation/issues", "Collate": "'combineScoreMatrixList.R' 'documentData.R'\n'genomation-classes.R' 'getRandomEnrichment.R'\n'findFeatureComb.R' 'patternMatrix.R' 'plotMatrix.R'\n'randomizeFeature.R' 'readAnnotate.R' 'readData.R'\n'scoreMatrix.R' 'scoreMatrixBin.R' 'scoreMatrixList.R' 'Ops.R'\n'test_genomation_package.R' 'deprecated_defunct.R'\n'enrichmentMatrix.R' 'RcppExports.R'", "RoxygenNote": "6.0.1.9000", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:16 UTC", "RemoteUrl": "https://github.com/bioc/genomation", "RemoteRef": "HEAD", "RemoteSha": "df3461e62825eee180f51d016929b5be6e802fb0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 08:16:47 UTC", "User": "root" }, "MD5sum": "690a986c7aa9fd651492cc6d66609dc4", "_user": "bioc", "_type": "src", "_file": "genomation_1.45.0.tar.gz", "_fileid": "ffeec59676975e15a0f3d50043dfe9918f4213b3423123b5785e2a1bf86a133a", "_filesize": 6268270, "_sha256": "ffeec59676975e15a0f3d50043dfe9918f4213b3423123b5785e2a1bf86a133a", "_created": "2026-05-30T08:16:47.000Z", "_published": "2026-05-30T11:54:24.436Z", "_jobs": [ { "job": 78636045657, "time": 225, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306787107" }, { "job": 78636045682, "time": 334, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306798079" }, { "job": 78636045691, "time": 486, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306812868" }, { "job": 78636045705, "time": 355, "config": "linux-release-arm64", 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method for a ScoreMatrixList object.", "topics": [ "[,ScoreMatrixList,ANY,ANY,ANY-method", "[,ScoreMatrixList-method" ] }, { "page": "annotateWithFeature-methods", "title": "Function to annotate given GRanges object with a given genomic feature", "topics": [ "annotateWithFeature", "annotateWithFeature,GRanges,GRanges-method" ] }, { "page": "annotateWithFeatureFlank-methods", "title": "Function to annotate a given GRanges object with promoter,exon,intron & intergenic values", "topics": [ "annotateWithFeatureFlank", "annotateWithFeatureFlank,GRanges,GRanges,GRanges-method" ] }, { "page": "annotateWithFeatures-methods", "title": "Annotate given ranges with genomic features", "topics": [ "annotateWithFeatures", "annotateWithFeatures,GRanges,GRangesList-method", "annotateWithFeatures,GRangesList,GRangesList-method" ] }, { "page": "annotateWithGeneParts-methods", "title": "Annotate given object with promoter, exon, intron and intergenic regions", "topics": [ "annotateWithGeneParts", "annotateWithGeneParts,GRanges,GRangesList-method", "annotateWithGeneParts,GRangesList,GRangesList-method" ] }, { "page": "AnnotationByFeature-class", "title": "An S4 class that information on overlap of target features with annotation features", "topics": [ "AnnotationByFeature-class" ] }, { "page": "AnnotationByGeneParts-class", "title": "An S4 class that information on overlap of target features with annotation features", "topics": [ "AnnotationByGeneParts-class" ] }, { "page": "binMatrix-methods", "title": "Bins the columns of a matrix using a user provided function", "topics": [ "binMatrix", "binMatrix,ScoreMatrix-method", "binMatrix,ScoreMatrixList-method" ] }, { "page": "c.ScoreMatrix", "title": "c.ScoreMatrix", "topics": [ "c.ScoreMatrix" ] }, { "page": "c.ScoreMatrixList", "title": "c.ScoreMatrixList", "topics": [ "c.ScoreMatrixList" ] }, { "page": "cage", "title": "Example CAGE data set.", "topics": [ "cage" ] }, { "page": "calculateOverlapSignificance-methods", "title": "function that calculates the significance of overlaps of two sets of features using randomization", "topics": [ "calculateOverlapSignificance", "calculateOverlapSignificance,GRanges,GRanges-method" ] }, { "page": "convertBed2Exons-methods", "title": "convert a data frame read-in from a bed file to a GRanges object for exons", "topics": [ "convertBed2Exons", "convertBed2Exons,data.frame-method" ] }, { "page": "convertBed2Introns-methods", "title": "convert a data frame read-in from a bed file to a GRanges object for introns", "topics": [ "convertBed2Introns", "convertBed2Introns,data.frame-method" ] }, { "page": "convertBedDf-methods", "title": "convert a data frame read-in from a bed file to a GRanges object", "topics": [ "convertBedDf", "convertBedDf,data.frame-method" ] }, { "page": "cpgi", "title": "Example CpG island data set.", "topics": [ "cpgi" ] }, { "page": "enrichmentMatrix-ScoreMatrix-method", "title": "Compute an enrichment of IP over control both stored in ScoreMatrix objects", "topics": [ "enrichmentMatrix", "enrichmentMatrix,ScoreMatrix,ScoreMatrix-method" ] }, { "page": "enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method", "title": "Compute an enrichment of IP (stored in ScoreMatrixList object) over control (stored in ScoreMatrix object)", "topics": [ "enrichmentMatrix,ScoreMatrixList,ScoreMatrix-method" ] }, { "page": "enrichmentMatrix-ScoreMatrixList-method", "title": "Compute an enrichment of IP over control both stored in ScoreMatrixList objects", "topics": [ "enrichmentMatrix,ScoreMatrixList,ScoreMatrixList-method" ] }, { "page": "findFeatureComb-methods", "title": "Find combitations of genomic features", "topics": [ "findFeatureComb", "findFeatureComb,GRangesList-method" ] }, { "page": "genes", "title": "Example RefSeq genes data set.", "topics": [ "genes" ] }, { "page": "AnnotationByGeneParts-methods", "title": "Get distance to nearest TSS and gene id from AnnotationByGeneParts", "topics": [ "AnnotationByGeneParts-method", "getAssociationWithTSS", "getAssociationWithTSS,", "getAssociationWithTSS,-methods", "getAssociationWithTSS,AnnotationByGeneParts-method" ] }, { "page": "getFeatsWithTargetsStats-methods", "title": "Get the percentage/count of annotation features overlapping with target features from AnnotationByFeature", "topics": [ "getFeatsWithTargetsStats", "getFeatsWithTargetsStats,AnnotationByFeature-method" ] }, { "page": "getFlanks-methods", "title": "Function to get upstream and downstream adjecent regions to a genomic feature such as CpG islands", "topics": [ "getFlanks", "getFlanks,GRanges-method" ] }, { "page": "getMembers-methods", "title": "Get the membership slot of AnnotationByFeature", "topics": [ "getMembers", "getMembers,AnnotationByFeature-method" ] }, { "page": "getRandomEnrichment-methods", "title": "get enrichment based on randomized feature overlap", "topics": [ "getRandomEnrichment", "getRandomEnrichment,GRanges,GRanges-method" ] }, { "page": "getTargetAnnotationStats-methods", "title": "Get the percentage of target features overlapping with annotation from AnnotationByFeature", "topics": [ "getTargetAnnotationStats", "getTargetAnnotationStats,AnnotationByFeature-method" ] }, { "page": "gffToGRanges", "title": "Converts a gff formated data.frame into a GenomicRanges object. The GenomicRanges object needs to be properly formated for the function to work.", "topics": [ "gffToGRanges" ] }, { "page": "heatMatrix", "title": "Draw a heatmap of a given ScoreMatrix object", "topics": [ "heatMatrix" ] }, { "page": "heatMeta", "title": "Heatmap for meta-region profiles", "topics": [ "heatMeta" ] }, { "page": "heatTargetAnnotation-methods", "title": "Plots the percentage of overlapping intervals with genomic features in a heatmap", "topics": [ "heatTargetAnnotation", "plotGeneAnnotation" ] }, { "page": "intersectScoreMatrixList-methods", "title": "Get common rows from all matrices in a ScoreMatrixList object", "topics": [ "intersectScoreMatrixList", "intersectScoreMatrixList,ScoreMatrixList-method" ] }, { "page": "multiHeatMatrix", "title": "Draw multiple heatmaps from a ScoreMatrixList object", "topics": [ "multiHeatMatrix" ] }, { "page": "Ops-numeric-ScoreMatrixList-method", "title": "Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.", "topics": [ "Ops,numeric,ScoreMatrixList-method" ] }, { "page": "Ops-ScoreMatrix-ScoreMatrix-method", "title": "Ops method for a ScoreMatrix object. It enables to use arithmetic, indicator and logic operations on ScoreMatrix objects.", "topics": [ "Ops,ScoreMatrix,ScoreMatrix-method" ] }, { "page": "Ops-ScoreMatrixList-numeric-method", "title": "Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.", "topics": [ "Ops,ScoreMatrixList,numeric-method" ] }, { "page": "Ops-ScoreMatrixList-ScoreMatrixList-method", "title": "Ops method for a ScoreMatrixList object. It enables to use arithmetic, indicator and logic operations on ScoreMatrixList objects.", "topics": [ "Ops,ScoreMatrixList,ScoreMatrixList-method" ] }, { "page": "orderBy-methods", "title": "Reorder all elements of a ScoreMatrixList to a given ordering vector", "topics": [ "orderBy", "orderBy,ScoreMatrixList-method" ] }, { "page": "patternMatrix-methods", "title": "Get scores that correspond to k-mer or PWM matrix occurrence for bases in each window", "topics": [ "patternMatrix", "patternMatrix,character,DNAStringSet,ANY-method", "patternMatrix,character,DNAStringSet-method", "patternMatrix,character,GRanges,BSgenome-method", "patternMatrix,list,DNAStringSet,ANY-method", "patternMatrix,list,DNAStringSet-method", "patternMatrix,list,GRanges,BSgenome-method", "patternMatrix,matrix,DNAStringSet,ANY-method", "patternMatrix,matrix,DNAStringSet-method", "patternMatrix,matrix,GRanges,BSgenome-method" ] }, { "page": "plotMeta", "title": "Line plot(s) for meta-region profiles", "topics": [ "plotMeta" ] }, { "page": "plotTargetAnnotation-methods", "title": "Plot annotation categories from AnnotationByGeneParts or AnnotationByFeature", "topics": [ "plotTargetAnnotation", "plotTargetAnnotation,AnnotationByFeature-method" ] }, { "page": "promoters", "title": "Example promoter data set.", "topics": [ "promoters" ] }, { "page": "RandomEnrichment-class", "title": "An S4 class for storing 'getRandomEnrichment' function results", "topics": [ "RandomEnrichment-class" ] }, { "page": "randomizeFeature-methods", "title": "function that randomizes the genomic coordinates", "topics": [ "randomizeFeature", "randomizeFeature,GRanges-method" ] }, { "page": "readBed", "title": "Read a BED file and convert it to GRanges.", "topics": [ "readBed" ] }, { "page": "readBroadPeak", "title": "A function to read the Encode formatted broad peak file into a GRanges object", "topics": [ "readBroadPeak" ] }, { "page": "readFeatureFlank-methods", "title": "A function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores", "topics": [ "readFeatureFlank", "readFeatureFlank,character-method" ] }, { "page": "readGeneric", "title": "Read a tabular file and convert it to GRanges.", "topics": [ "readGeneric" ] }, { "page": "readNarrowPeak", "title": "A function to read the Encode formatted narrowPeak file into a GRanges object", "topics": [ "readNarrowPeak" ] }, { "page": "readTranscriptFeatures-methods", "title": "Function for reading exon intron and promoter structure from a given bed file", "topics": [ "readTranscriptFeatures", "readTranscriptFeatures,character-method" ] }, { "page": "scaleScoreMatrix-methods", "title": "Scales the values in the matrix by rows and/or columns", "topics": [ "scaleScoreMatrix", "scaleScoreMatrix,ScoreMatrix-method" ] }, { "page": "scaleScoreMatrixList", "title": "Scale the ScoreMatrixList", "topics": [ "scaleScoreMatrixList", "scaleScoreMatrixList,ScoreMatrixList-method" ] }, { "page": 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