{ "_id": "6a17dfacacfb0bcc41d9e5de", "Package": "deltaCaptureC", "Title": "This Package Discovers Meso-scale Chromatin Remodeling from 3C\nData", "Version": "1.27.0", "Authors@R": "person(given = \"Michael\",\nfamily = \"Shapiro\",\nrole = c(\"aut\", \"cre\"),\nemail = \"michael.shapiro@crick.ac.uk\",\ncomment = c(ORCID = \"0000-0002-2769-9320\"))", "Description": "This package discovers meso-scale chromatin remodelling\nfrom 3C data. 3C data is local in nature. It givens\ninteraction counts between restriction enzyme digestion\nfragments and a preferred 'viewpoint' region. By binning this\ndata and using permutation testing, this package can test\nwhether there are statistically significant changes in the\ninteraction counts between the data from two cell types or two\ntreatments.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3.9000", "VignetteBuilder": "knitr", "biocViews": "BiologicalQuestion, StatisticalMethod", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:50 UTC", "RemoteUrl": "https://github.com/bioc/deltaCaptureC", "RemoteRef": "HEAD", "RemoteSha": "0d56b65b9f037db9b5fa64312bcdcfcc698cef28", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:17:10 UTC", "User": "root" }, "Author": "Michael Shapiro [aut, cre] (ORCID:\n)", "Maintainer": "Michael Shapiro ", "MD5sum": "471a37d0a4c6e68fc020c76a83f99ba5", "_user": "bioc", "_type": "src", "_file": "deltaCaptureC_1.27.0.tar.gz", 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"email": "michael.shapiro@crick.ac.uk", "orcid": "0000-0002-2769-9320" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "tictoc", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "biologicalquestion", "statisticalmethod" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 312, "source": "https://www.bioconductor.org/packages/stats/bioc/deltaCaptureC" }, "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/deltaCaptureC.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "binSummarizedExperiment", "downshiftDFtoMatrix", "generatePermutation", "getDeltaSE", "getLopsidedness", "getMeanNormalizedCountsSE", "getNormalizedCountsSE", "getOverlapWeights", "getPValueCutoff", "getRunAndLopsidednessStatistics", "getRunStatisticsDist", "getRunTotals", "getSignificantRegions", "getSizeFactorsDF", "getSizeFactorsSE", "plotSignificantRegions", "rebinToMultiple" ], "_datasets": [ { "name": "bigBinSize", "title": "Big bin size", "object": "bigBinSize", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "binnedDeltaPlot", "title": "Plot of Binned Delta Counts", "object": "binnedDeltaPlot", "class": [ "gg", "ggplot" ], "fields": [], "table": false, "tojson": false }, { "name": "binnedDeltaSE", "title": "Binned difference of mean capture-C counts between EScells and Neurons", "object": "binnedDeltaSE", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "binnedSummarizedExperiment", "title": "Binned Capture-C counts of EScells and Neurons", "object": "binnedSummarizedExperiment", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "deltaSE", "title": "Difference of mean capture-C counts between EScells and Neurons", "object": "deltaSE", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "miniDeltaSE", "title": "Difference of mean capture-C counts between EScells and Neurons", "object": "miniDeltaSE", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "miniSE", "title": "Capture-C counts of EScells and Neurons", "object": "miniSE", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "miniSEDF", "title": "Capture-C counts of EScells and Neurons", "object": "miniSEDF", "class": [ "data.frame" ], "fields": [ "chr", "start", "emd", "PauparTSS.EScells_1", "PauparTSS.EScells_2", "PauparTSS.Neu_1", "PauparTSS.Neu_2" ], "rows": 1909, "table": true, "tojson": true }, { "name": "numPermutations", "title": "Number of permutations used in example permutation testing.", "object": "numPermutations", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "plotTitle", "title": "Title for delta capture-C plot", "object": "plotTitle", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "pValue", "title": "P-value", "object": "pValue", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "regionOfInterest", "title": "Region of interest surrounding the viewpoint", "object": "regionOfInterest", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "significanceType", "title": "Type for testing significance", "object": "significanceType", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "significantRegions", "title": "Regions of significant remodeling in example data", "object": "significantRegions", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "significantRegionsPlot", "title": "A plot of the significant regions in the sample data.", "object": "significantRegionsPlot", "class": [ "gg", "ggplot" ], "fields": [], "table": false, "tojson": false }, { "name": "smallBins", "title": "Small Bins", "object": "smallBins", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "smallBinSize", "title": "Small Bin Size", "object": "smallBinSize", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "smallerDeltaSE", "title": "A subset of miniDeltaSE.", "object": "smallerDeltaSE", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "smallSetOfSmallBins", "title": "Small Bins", "object": "smallSetOfSmallBins", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "viewpointRegion", "title": "Region surrounding the viewpoint", "object": "viewpointRegion", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "weightsExampleBins", "title": "Weights example bins", "object": "weightsExampleBins", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "weightsExampleGr", "title": "Weights example", "object": "weightsExampleGr", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dot-getRunsAndTotals", "title": "A helper function for getRunTotals", "topics": [ ".getRunsAndTotals" ] }, { "page": "bigBinSize", "title": "Big bin size", "topics": [ "bigBinSize" ] }, { "page": "binnedDeltaPlot", "title": "Plot of Binned Delta Counts", "topics": [ "binnedDeltaPlot" ] }, { "page": "binnedDeltaSE", "title": "Binned difference of mean capture-C counts between EScells and Neurons", "topics": [ "binnedDeltaSE" ] }, { "page": "binnedSummarizedExperiment", "title": "Binned Capture-C counts of EScells and Neurons", "topics": [ "binnedSummarizedExperiment" ] }, { "page": "binSummarizedExperiment", "title": "Bin a Summarized experiment into a set of bins given by a GRanges object", "topics": [ "binSummarizedExperiment" ] }, { "page": "deltaSE", "title": "Difference of mean capture-C counts between EScells and Neurons", "topics": [ "deltaSE" ] }, { "page": "downshiftDFtoMatrix", "title": "Downshift from DF to matrix", "topics": [ "downshiftDFtoMatrix" ] }, { "page": "generatePermutation", "title": "Generate permutation for permutation testing", "topics": [ "generatePermutation" ] }, { "page": "getDeltaSE", "title": "Make delta summarized experiment:", "topics": [ "getDeltaSE" ] }, { "page": "getLopsidedness", "title": "Get the lopsidedness statistic", "topics": [ "getLopsidedness" ] }, { "page": "getMeanNormalizedCountsSE", "title": "Make mean treatment summarized experiment:", "topics": [ "getMeanNormalizedCountsSE" ] }, { "page": "getNormalizedCountsSE", "title": "Get normalized counts", "topics": [ "getNormalizedCountsSE" ] }, { "page": "getOverlapWeights", "title": "Get the binning factors for one set of GRanges into another", "topics": [ "getOverlapWeights" ] }, { "page": "getPValueCutoff", "title": "This function returns the significance levels for min, max, \"abs\" and lopsidedness.", "topics": [ "getPValueCutoff" ] }, { "page": "getRunAndLopsidednessStatistics", "title": "Get the distribution of run and lopsidedness statistics", "topics": [ "getRunAndLopsidednessStatistics" ] }, { "page": "getRunStatistics", "title": "This function is called by getRunsStatisticsDist on the individual elements of a list of scrambled runs.", "topics": [ "getRunStatistics" ] }, { "page": "getRunStatisticsDist", "title": "This takes a list of (scrambled) runs and returns their run statistics", "topics": [ "getRunStatisticsDist" ] }, { "page": "getRunTotals", "title": "Get the runs and their values", "topics": [ "getRunTotals" ] }, { "page": "getSignificantRegions", "title": "Get ths significant regions from delta data", "topics": [ "getSignificantRegions" ] }, { "page": "getSizeFactorsDF", "title": "Get the size factors for count normalization", "topics": [ "getSizeFactorsDF" ] }, { "page": "getSizeFactorsSE", "title": "Get the size factors for SummarizedExperiment", "topics": [ "getSizeFactorsSE" ] }, { "page": "miniDeltaSE", "title": "Difference of mean capture-C counts between EScells and Neurons", "topics": [ "miniDeltaSE" ] }, { "page": "miniSE", "title": "Capture-C counts of EScells and Neurons", "topics": [ "miniSE" ] }, { "page": "miniSEDF", "title": "Capture-C counts of EScells and Neurons", "topics": [ "miniSEDF" ] }, { "page": "numPermutations", "title": "Number of permutations used in example permutation testing.", "topics": [ "numPermutations" ] }, { "page": "plotSignificantRegions", "title": "This produces a plot of the region of interest showing regions of significance.", "topics": [ "plotSignificantRegions" ] }, { "page": "plotTitle", "title": "Title for delta capture-C plot", "topics": [ "plotTitle" ] }, { "page": "pValue", "title": "P-value", "topics": [ "pValue" ] }, { "page": "rebinToMultiple", "title": "Rebin a SummarizedExperiment to a multiple of its bin width", "topics": [ "rebinToMultiple" ] }, { "page": "regionOfInterest", "title": "Region of interest surrounding the viewpoint", "topics": [ "regionOfInterest" ] }, { "page": "significanceType", "title": "Type for testing significance", "topics": [ "significanceType" ] }, { "page": "significantRegions", "title": "Regions of significant remodeling in example data", "topics": [ "significantRegions" ] }, { "page": "significantRegionsPlot", "title": "A plot of the significant regions in the sample data.", "topics": [ "significantRegionsPlot" ] }, { "page": "smallBins", "title": "Small Bins", "topics": [ "smallBins" ] }, { "page": "smallBinSize", "title": "Small Bin Size", "topics": [ "smallBinSize" ] }, { "page": "smallerDeltaSE", "title": "A subset of miniDeltaSE.", "topics": [ "smallerDeltaSE" ] }, { "page": "smallSetOfSmallBins", "title": "Small Bins", "topics": [ "smallSetOfSmallBins" ] }, { "page": "viewpointRegion", "title": "Region surrounding the viewpoint", "topics": [ "viewpointRegion" ] }, { "page": "weightsExampleBins", "title": "Weights example bins", "topics": [ "weightsExampleBins" ] }, { "page": "weightsExampleGr", "title": "Weights example", "topics": [ "weightsExampleGr" ] } ], "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "cli", "codetools", "cpp11", "DelayedArray", "DESeq2", "farver", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "tictoc", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "deltaCaptureC.Rmd", "filename": "deltaCaptureC.html", "title": "Delta Capure-C", "author": "Michael Shapiro", "engine": "knitr::rmarkdown", "headings": [ "deltaCaptureC", "Introduction", "Difference in mean normalized counts:", "The Algorithm", "Invoking the algorithm and plotting the results", "Under the hood", "Normalization", "" ], "created": "2019-04-23 14:30:30", "modified": 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