Package: mariner 1.7.0
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_1.7.0.tar.gz
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mariner.pdf |mariner.html✨
mariner/json (API)
NEWS
| # Install 'mariner' in R: |
| install.packages('mariner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:mariner-1.5.0(bioc 3.20)mariner-1.4.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
functionalgenomicsvisualizationhic
Last updated 23 days agofrom:58efcf68f4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:adjustEnrichmentaggHicMatricesaggPairMcolsas_ginteractionsbinPairsbinRangescalcLoopEnrichmentcbindchangePixelRescountscounts<-end1end2getPairClustershdf5BlockApplyInteractionArrayInteractionMatrixmakeGInteractionsFromDataFrameMatrixSelectionMergedGInteractionsmergePairspathpath<-pixelsToMatricesplotEnrichmentplotMatrixpullHicMatricespullHicPixelsrbindremoveShortPairsselectBlockselectBottomLeftselectBottomRightselectCenterPixelselectColsselectCoordinatesselectCornersselectInnerselectionMethodselectOuterselectPixelselectRadiusselectRowsselectSubmatrixselectTopLeftselectTopRightseqnames1seqnames2shiftRangesshowsnapToBinssourcesstart1start2subsetBySource
Dependencies:abindaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsclicodetoolscolorspacecolourvaluescpp11crayoncurldata.tabledbscanDelayedArraydigestdplyrfansifarverformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggplotifygluegridGraphicsgtableHDF5ArrayhmshttrInteractionSetIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplotgardenerplyrangesprettyunitsprogresspurrrR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystrawrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlyulab.utilszlibbioc
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 | aggPairMcols aggPairMcols,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 | binPairs binPairs,DF_OR_df_OR_dt,numeric,character_OR_numeric_OR_missing,character_OR_numeric_OR_missing-method binPairs,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 |
| Change pixels from one resolution to another selecting the new pixel using Hi-C data. | changePixelRes changePixelRes,GInteractions,character-method |
| Access count matrices from InteractionArray or InteractionMatrix | counts,InteractionArray-method counts,InteractionMatrix-method counts<-,InteractionMatrix-method |
| Get clustered pairs from MergedGInteractions object | getPairClusters getPairClusters,MergedGInteractions-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 |
| InteractionMatrix Class | cbind,InteractionMatrix-method InteractionMatrix InteractionMatrix,ANY,GInteractions-method InteractionMatrix,missing,missing-method InteractionMatrix-class rbind,InteractionMatrix-method show,InteractionMatrix-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 |
| 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 |
| 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 |
| 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 |
| Subset MergedGInteractions by source | subsetBySource subsetBySource,MergedGInteractions,character_OR_missing,character_OR_missing-method subsetBySource,MergedGInteractions,character_OR_missing,missing-method subsetBySource,MergedGInteractions,missing,character_OR_missing-method subsetBySource,MergedGInteractions,missing,missing-method |
