Package: mariner 1.13.0
Eric Davis
mariner: Mariner: Explore the Hi-Cs
Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.
Authors:
mariner_1.13.0.tar.gz
mariner_1.13.0.zip(r-4.7)mariner_1.13.0.zip(r-4.6)mariner_1.13.0.zip(r-4.5)
mariner_1.13.0.tgz(r-4.6-any)mariner_1.13.0.tgz(r-4.5-any)
mariner_1.13.0.tar.gz(r-4.7-any)mariner_1.13.0.tar.gz(r-4.6-any)
mariner_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
mariner/json (API)
NEWS
| # Install 'mariner' in R: |
| install.packages('mariner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ericsdavis/mariner/issues
Pkgdown/docs site:https://ericscottdavis.com
On BioConductor:mariner-1.13.0(bioc 3.24)mariner-1.12.0(bioc 3.23)
functionalgenomicsvisualizationhic
Last updated from:9d72228e87. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 260 | ||
| linux-devel-x86_64 | ERROR | 759 | ||
| source / vignettes | OK | 420 | ||
| linux-release-x86_64 | ERROR | 753 | ||
| macos-release-arm64 | ERROR | 578 | ||
| macos-oldrel-arm64 | ERROR | 616 | ||
| windows-devel | ERROR | 1400 | ||
| windows-release | ERROR | 1392 | ||
| windows-oldrel | ERROR | 1553 | ||
| wasm-release | OK | 207 |
Exports:adjustEnrichmentaggHicMatricesaggMetadataas_ginteractionsas.listassignToBinsbinRangescalcLoopEnrichmentcbindchangePixelResclusterscolDatacountOverlapscountscounts<-defaultBufferend1end2findOverlapshdf5BlockApplyInteractionArrayInteractionJaggedArrayInteractionMatrixinteractionsJaggedArraymakeGInteractionsFromDataFramemakeRandomGInteractionsmakeRandomGRangesMatrixSelectionMergedGInteractionsmergePairsmetadataoverlapsAnypathpath<-pileupBoundariespileupDomainspileupPixelspixelsToMatricesplotEnrichmentplotMatrixpullHicMatricespullHicPixelsrbindregularizeremoveShortPairsselectBlockselectBottomLeftselectBottomRightselectCenterPixelselectColsselectCoordinatesselectCornersselectInnerselectionMethodselectOuterselectPixelselectRadiusselectRowsselectSubmatrixselectTopLeftselectTopRightseqnames1seqnames2setsshiftRangesshowsnapToBinssourcesstart1start2subsetByOverlaps
Dependencies:abindaskpassassertthatBHBiobaseBiocBaseUtilsBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitopscigarilloclicodetoolscolourvaluescpp11crayoncurldata.tabledbscanDelayedArraydigestdir.expirydplyrfarverfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2ggplotifygluegridGraphicsgtableh5mreadHDF5ArrayhmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplotgardenerplyrangesprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystrawrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Mariner: Explore the Hi-Cs | mariner-package mariner |
| Aggregate count matrices from InteractionArray objects | aggHicMatrices aggHicMatrices,InteractionArray-method |
| Aggregate the metadata columns of merged pairs | aggMetadata aggMetadata,MergedGInteractions,character,character_OR_function_OR_list-method |
| Convert DataFrames to GInteraction objects | as_ginteractions as_ginteractions,DF_OR_df_OR_dt,logical_OR_missing,logical_OR_missing-method makeGInteractionsFromDataFrame makeGInteractionsFromDataFrame,DF_OR_df_OR_dt,logical_OR_missing,logical_OR_missing-method |
| Flexibly bin paired ranges | assignToBins assignToBins,DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method assignToBins,GInteractions,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method |
| Flexibly bin ranges | binRanges binRanges,GRanges,numeric,character_OR_numeric_OR_missing-method |
| Calculate loop enrichment over background. | calcLoopEnrichment calcLoopEnrichment,GInteractions,character-method calcLoopEnrichment,InteractionArray,missing-method |
| Change pixels from one resolution to another selecting the new pixel using Hi-C data. | changePixelRes changePixelRes,GInteractions,character-method |
| Get clustered pairs from MergedGInteractions object | clusters clusters,MergedGInteractions-method |
| Access count matrices from InteractionArray or InteractionMatrix | counts,InteractionArray-method counts,InteractionMatrix-method counts<-,InteractionMatrix-method |
| Return default buffer If InteractionArray is supplied, it uses the dimensions of counts matrices to set the buffer dimensions. | defaultBuffer |
| Overlap methods for InteractionJaggedArray | countOverlaps countOverlaps,InteractionJaggedArray,InteractionJaggedArray-method countOverlaps,InteractionJaggedArray,missing-method countOverlaps,InteractionJaggedArray,Vector-method findOverlaps findOverlaps,InteractionJaggedArray,InteractionJaggedArray-method findOverlaps,InteractionJaggedArray,missing-method findOverlaps,InteractionJaggedArray,Vector-method overlapsAny overlapsAny,InteractionJaggedArray,InteractionJaggedArray-method overlapsAny,InteractionJaggedArray,missing-method overlapsAny,InteractionJaggedArray,Vector-method subsetByOverlaps subsetByOverlaps,InteractionJaggedArray,InteractionJaggedArray-method subsetByOverlaps,InteractionJaggedArray,missing-method subsetByOverlaps,InteractionJaggedArray,Vector-method |
| HDF5-backed blockApply | hdf5BlockApply hdf5BlockApply,DelayedArray-method |
| InteractionArray Class | cbind,InteractionArray-method InteractionArray InteractionArray,ANY,GInteractions-method InteractionArray,missing,missing-method InteractionArray-class rbind,InteractionArray-method show,InteractionArray-method |
| InteractionJaggedArray Class | 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 |
| InteractionMatrix Class | cbind,InteractionMatrix-method InteractionMatrix InteractionMatrix,ANY,GInteractions-method InteractionMatrix,missing,missing-method InteractionMatrix-class rbind,InteractionMatrix-method show,InteractionMatrix-method |
| JaggedArray Class | as.list,JaggedArray-method dim,JaggedArray-method JaggedArray JaggedArray-class path,JaggedArray-method show,JaggedArray-method [,JaggedArray,ANY,ANY,ANY-method |
| Creating random GRanges & GInteractions | makeRandomGInteractions makeRandomGInteractions,Seqinfo-method makeRandomGRanges makeRandomGRanges,Seqinfo-method |
| MatrixSelection Class | MatrixSelection MatrixSelection-class |
| MergedGInteractions Class | MergedGInteractions MergedGInteractions-class |
| Merge sets of paired interactions | mergePairs mergePairs,list_OR_SimpleList_OR_GInteractions,numeric-method |
| Accessor for h5File path from an InteractionMatrix | path,InteractionMatrix-method path<-,InteractionMatrix-method |
| Pileup Hi-C contacts around boundary regions | pileupBoundaries pileupBoundaries,GRanges_OR_GInteractions,character,numeric-method |
| Pileup Hi-C domains | pileupDomains pileupDomains,GRanges_OR_GInteractions,character,numeric-method |
| Pileup Hi-C pixels | pileupPixels pileupPixels,GInteractions,character,numeric-method |
| Expand pixels to submatrices | pixelsToMatrices pixelsToMatrices,GInteractions,numeric-method |
| Adjust loop enrichment to remove distance- dependent effect. | adjustEnrichment adjustEnrichment,DelayedMatrix_OR_matrix,GInteractions-method plotEnrichment plotEnrichment,numeric,GInteractions-method |
| Plot matrix | plotMatrix plotMatrix,DelayedMatrix_OR_matrix-method |
| Pull submatrices from `.hic` files | pullHicMatrices pullHicMatrices,GInteractions,character,numeric-method |
| Pull contact frequency from `.hic` files | pullHicPixels pullHicPixels,GInteractions,character,numeric-method |
| Regularize JaggedArray or InteractionJaggedArray objects | regularize regularize,InteractionJaggedArray-method regularize,JaggedArray-method |
| Remove interactions that would cross the Hi-C diagonal or a specified distance from the diagonal. | removeShortPairs removeShortPairs,GInteractions-method |
| Get selectionMethod from MergedGInteractions object | selectionMethod selectionMethod,MergedGInteractions-method |
| Get the pixel representing the strongest or weakest interaction in an InteractionArray | selectPixel selectPixel,InteractionArray-method |
| Visualize selection for a MatrixSelection object | 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 |
| Access each portion of a GInteractions-like object | end1 end1,GInteractions_OR_InteractionSet-method end2 end2,GInteractions_OR_InteractionSet-method seqnames1 seqnames1,GInteractions_OR_InteractionSet-method seqnames2 seqnames2,GInteractions_OR_InteractionSet-method start1 start1,GInteractions_OR_InteractionSet-method start2 start2,GInteractions_OR_InteractionSet-method |
| Get each set from a MergedGInteractions object | sets sets,MergedGInteractions,character_OR_missing,character_OR_missing-method sets,MergedGInteractions,character_OR_missing,missing-method sets,MergedGInteractions,missing,character_OR_missing-method sets,MergedGInteractions,missing,missing-method |
| Flexibly shifting GRanges according to strand | shiftRanges shiftRanges,GRanges,character_OR_numeric-method |
| Snap GRanges or GInteractions to nearest bins | snapToBins snapToBins,GInteractions,numeric-method snapToBins,GRanges,numeric-method |
| Accessor for sources | sources sources,MergedGInteractions-method |
