{ "_id": "6ae7707a9ceaa78f2009a186", "Package": "mariner", "Type": "Package", "Title": "Mariner: Explore the Hi-Cs", "Version": "1.13.1", "Authors@R": "c(\nperson(\"Eric\", \"Davis\", role = c(\"aut\", \"cre\"),\nemail = \"ericscottdavis@outlook.com\",\ncomment = c(ORCID = \"0000-0003-4051-3217\")),\nperson(\"Sarah\", \"Parker\", role = c(\"aut\"),\nemail = \"smp3800@gmail.com\",\ncomment = c(ORCID = \"0000-0002-2700-3979\"))\n)", "Description": "Tools for manipulating paired ranges and working with Hi-C\ndata in R. 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selecting the new pixel using Hi-C data.", "topics": [ "changePixelRes", "changePixelRes,GInteractions,character-method" ] }, { "page": "clusters", "title": "Get clustered pairs from MergedGInteractions object", "topics": [ "clusters", "clusters,MergedGInteractions-method" ] }, { "page": "coolStraw", "title": "Equivalent to `strawr::straw` for `.cool` and `.mcool` files", "topics": [ "coolStraw" ] }, { "page": "counts", "title": "Access count matrices from InteractionArray or InteractionMatrix", "topics": [ "counts,InteractionArray-method", "counts,InteractionMatrix-method", "counts<-,InteractionMatrix-method" ] }, { "page": "defaultBuffer", "title": "Return default buffer If InteractionArray is supplied, it uses the dimensions of counts matrices to set the buffer dimensions.", "topics": [ "defaultBuffer" ] }, { "page": "InteractionJaggedArray-overlaps", "title": "Overlap methods for InteractionJaggedArray", "topics": [ "countOverlaps", 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"cbind,InteractionArray-method", "InteractionArray", "InteractionArray,ANY,GInteractions-method", "InteractionArray,missing,missing-method", "InteractionArray-class", "rbind,InteractionArray-method", "show,InteractionArray-method" ] }, { "page": "InteractionJaggedArray-class", "title": "InteractionJaggedArray Class", "topics": [ "colData,InteractionJaggedArray-method", "counts,InteractionJaggedArray-method", "dim,InteractionJaggedArray-method", "InteractionJaggedArray", "InteractionJaggedArray-class", "interactions,InteractionJaggedArray-method", "length,InteractionJaggedArray-method", "metadata,InteractionJaggedArray-method", "path,InteractionJaggedArray-method", "show,InteractionJaggedArray-method", "[,InteractionJaggedArray,ANY,ANY,ANY-method" ] }, { "page": "InteractionMatrix-class", "title": "InteractionMatrix Class", "topics": [ "cbind,InteractionMatrix-method", "InteractionMatrix", "InteractionMatrix,ANY,GInteractions-method", "InteractionMatrix,missing,missing-method", "InteractionMatrix-class", "rbind,InteractionMatrix-method", "show,InteractionMatrix-method" ] }, { "page": "JaggedArray-class", "title": "JaggedArray Class", "topics": [ "as.list,JaggedArray-method", "dim,JaggedArray-method", "JaggedArray", "JaggedArray-class", "path,JaggedArray-method", "show,JaggedArray-method", "[,JaggedArray,ANY,ANY,ANY-method" ] }, { "page": "makeRandomGInteractions", "title": "Creating random GRanges & GInteractions", "topics": [ "makeRandomGInteractions", "makeRandomGInteractions,Seqinfo-method", "makeRandomGRanges", "makeRandomGRanges,Seqinfo-method" ] }, { "page": "MatrixSelection-class", "title": "MatrixSelection Class", "topics": [ "MatrixSelection", "MatrixSelection-class" ] }, { "page": "MergedGInteractions-class", "title": "MergedGInteractions Class", "topics": [ "MergedGInteractions", "MergedGInteractions-class" ] }, { "page": "mergePairs", "title": "Merge sets of paired interactions", "topics": [ "mergePairs", "mergePairs,list_OR_SimpleList_OR_GInteractions,numeric-method" ] }, { "page": "path", "title": "Accessor for h5File path from an InteractionMatrix", "topics": [ "path,InteractionMatrix-method", "path<-,InteractionMatrix-method" ] }, { "page": "pileupBoundaries", "title": "Pileup Hi-C contacts around boundary regions", "topics": [ "pileupBoundaries", "pileupBoundaries,GRanges_OR_GInteractions,character,numeric-method" ] }, { "page": "pileupDomains", "title": "Pileup Hi-C domains", "topics": [ "pileupDomains", "pileupDomains,GRanges_OR_GInteractions,character,numeric-method" ] }, { "page": "pileupPixels", "title": "Pileup Hi-C pixels", "topics": [ "pileupPixels", "pileupPixels,GInteractions,character,numeric-method" ] }, { "page": "pixelsToMatrices", "title": "Expand pixels to submatrices", "topics": [ "pixelsToMatrices", "pixelsToMatrices,GInteractions,numeric-method" ] }, { "page": "adjustEnrichment", "title": "Adjust loop enrichment to remove distance- dependent effect.", "topics": [ "adjustEnrichment", "adjustEnrichment,DelayedMatrix_OR_matrix,GInteractions-method", "plotEnrichment", "plotEnrichment,numeric,GInteractions-method" ] }, { "page": "plotMatrix", "title": "Plot matrix", "topics": [ "plotMatrix", "plotMatrix,DelayedMatrix_OR_matrix-method" ] }, { "page": "pullHicMatrices", "title": "Pull submatrices from Hi-C files", "topics": [ "pullHicMatrices", "pullHicMatrices,GInteractions,character,numeric-method" ] }, { "page": "pullHicPixels", "title": "Pull contact frequency from Hi-C files", "topics": [ "pullHicPixels", "pullHicPixels,GInteractions,character,numeric-method" ] }, { "page": "readCoolBpResolutions", "title": "Function for reading basepair resolutions from .cool or .mcool file", "topics": [ "readCoolBpResolutions" ] }, { "page": "readCoolChroms", "title": "Function for reading chromosomes from a `.cool` or `.mcool` file", "topics": [ "readCoolChroms" ] }, { "page": "readCoolNormTypes", "title": "Function for reading available normalizations from .cool or .mcool file", "topics": [ "readCoolNormTypes" ] }, { "page": "regularize", "title": "Regularize JaggedArray or InteractionJaggedArray objects", "topics": [ "regularize", "regularize,InteractionJaggedArray-method", "regularize,JaggedArray-method" ] }, { "page": "removeShortPairs", "title": "Remove interactions that would cross the Hi-C diagonal or a specified distance from the diagonal.", "topics": [ "removeShortPairs", "removeShortPairs,GInteractions-method" ] }, { "page": "selectionMethod", "title": "Get selectionMethod from MergedGInteractions object", "topics": [ "selectionMethod", "selectionMethod,MergedGInteractions-method" ] }, { "page": "selectPixel", "title": "Get the pixel representing the strongest or weakest interaction in an InteractionArray", "topics": [ "selectPixel", "selectPixel,InteractionArray-method" ] }, { "page": "selection-functions", "title": "Visualize selection for a MatrixSelection object", "topics": [ "selectBlock", "selectBlock,numeric-method", "selectBottomLeft", "selectBottomLeft,numeric-method", "selectBottomRight", "selectBottomRight,numeric-method", "selectCenterPixel", "selectCenterPixel,numeric-method", "selectCols", "selectCols,numeric-method", "selectCoordinates", "selectCoordinates,numeric-method", "selectCorners", "selectCorners,numeric-method", "selectInner", "selectInner,numeric-method", "selectOuter", "selectOuter,numeric-method", "selectRadius", "selectRadius,numeric-method", "selectRows", "selectRows,numeric-method", "selectSubmatrix", "selectSubmatrix,matrix-method", "selectTopLeft", "selectTopLeft,numeric-method", "selectTopRight", "selectTopRight,numeric-method", "show,MatrixSelection-method" ] }, { "page": "GInteractions-accessors", "title": "Access each portion of a GInteractions-like object", "topics": [ "end1", "end1,GInteractions_OR_InteractionSet-method", "end2", "end2,GInteractions_OR_InteractionSet-method", "seqnames1", "seqnames1,GInteractions_OR_InteractionSet-method", "seqnames2", 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