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:Eric Davis [aut, cre], Sarah Parker [aut]

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✨
DESCRIPTION |NEWS
card.svg |card.png
mariner/json (API)

# 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)

functionalgenomics visualization hic

7.24 score 12 stars 193 scripts 284 downloads 72 exports 101 dependencies

Last updated from:9d72228e87. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
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:adjustEnrichment aggHicMatrices aggMetadata as_ginteractions as.list assignToBins binRanges calcLoopEnrichment cbind changePixelRes clusters colData countOverlaps counts counts<-defaultBuffer end1 end2 findOverlaps hdf5BlockApply InteractionArray InteractionJaggedArray InteractionMatrix interactions JaggedArray makeGInteractionsFromDataFrame makeRandomGInteractions makeRandomGRanges MatrixSelection MergedGInteractions mergePairs metadata overlapsAny path path<-pileupBoundaries pileupDomains pileupPixels pixelsToMatrices plotEnrichment plotMatrix pullHicMatrices pullHicPixels rbind regularize removeShortPairs selectBlock selectBottomLeft selectBottomRight selectCenterPixel selectCols selectCoordinates selectCorners selectInner selectionMethod selectOuter selectPixel selectRadius selectRows selectSubmatrix selectTopLeft selectTopRight seqnames1 seqnames2 sets shiftRanges show snapToBins sources start1 start2 subsetByOverlaps

Dependencies:abind askpass assertthat BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bitops cigarillo cli codetools colourvalues cpp11 crayon curl data.table dbscan DelayedArray digest dir.expiry dplyr farver filelock formatR fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 ggplotify glue gridGraphics gtable h5mread HDF5Array hms httr InteractionSet IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plotgardener plyranges prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray strawr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml yulab.utils

Introduction to mariner

Rendered frommariner.Rmdusingknitr::rmarkdown

Last update: 2025-08-05
Started: 2025-08-05

Citation

Development and contributors

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