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A B C D F G H I K L M N P Q R S T U misc
| diffloop-package | diffloop: A package for differential DNA loop calling from ChIA-PET data |
| addchr | Add 'chr' to GRanges seqnames |
| addchr-method | Add 'chr' to GRanges seqnames |
| annotateAnchors | Add meta data column to anchors based on GRanges |
| annotateAnchors-method | Add meta data column to anchors based on GRanges |
| annotateAnchors.bed | Add meta data column to anchors based on bedgraph scores |
| annotateAnchors.bed-method | Add meta data column to anchors based on bedgraph scores |
| annotateAnchors.bigwig | Add meta data column to anchors based on .bigwig |
| annotateAnchors.bigwig-method | Add meta data column to anchors based on .bigwig |
| annotateLoops | Annotate loops as Enhancer-Promoter or CTCF-CTCF |
| annotateLoops-method | Annotate loops as Enhancer-Promoter or CTCF-CTCF |
| annotateLoops.dge | Annotate enhancer-promoter loops with differential gene expression |
| annotateLoops.dge-method | Annotate enhancer-promoter loops with differential gene expression |
| bedToGRanges | Read a file and make a GRanges object |
| bedToGRanges-method | Read a file and make a GRanges object |
| calcLDSizeFactors | Compute normalizing factors for each sample |
| calcLDSizeFactors-method | Compute normalizing factors for each sample |
| callCCDs | Compute Chromatin Contact Domains (CCDs) |
| callCCDs-method | Compute Chromatin Contact Domains (CCDs) |
| computeBoundaryScores | Compute boundary scores for genomic loci in between anchors |
| computeBoundaryScores-method | Compute boundary scores for genomic loci in between anchors |
| diffloop | diffloop: A package for differential DNA loop calling from ChIA-PET data |
| dim-method | See dimensions of loops object |
| featureTest | Combined association test for all loops in a defined region |
| featureTest-method | Combined association test for all loops in a defined region |
| filterLoops | Filter loops |
| filterLoops-method | Filter loops |
| filterSpanningLoops | Retain loops spanning some genomic feature |
| filterSpanningLoops-method | Retain loops spanning some genomic feature |
| geneinfo | Human/mouse exon locations |
| getHumanGenes | Get protein coding gene regions |
| getHumanGenes-method | Get protein coding gene regions |
| getHumanTSS | Get Human Transcription Start Sites |
| getHumanTSS-method | Get Human Transcription Start Sites |
| getMouseGenes | Get protein coding gene regions |
| getMouseGenes-method | Get protein coding gene regions |
| getMouseTSS | Get Mouse Transcription Start Sites |
| getMouseTSS-method | Get Mouse Transcription Start Sites |
| head-method | Extract first part of loops object |
| human.genes | Human protein coding genes |
| interchromosomal | Loops between chromosomes |
| interchromosomal-method | Loops between chromosomes |
| intrachromosomal | Loops within chromosomes |
| intrachromosomal-method | Loops within chromosomes |
| keepCTCFloops | Keep CTCF loops |
| keepCTCFloops-method | Keep CTCF loops |
| keepEPloops | Keep enhancer-promoter loops |
| keepEPloops-method | Keep enhancer-promoter loops |
| loopAssoc | Generalized differential Loop Calling |
| loopAssoc-method | Generalized differential Loop Calling |
| loopDistancePlot | Visualize proportion of loops at distances |
| loopDistancePlot-method | Visualize proportion of loops at distances |
| loopGenes | Determine genes contained within loops |
| loopGenes-method | Determine genes contained within loops |
| loopMetrics | Types of loops |
| loopMetrics-method | Types of loops |
| loopPlot | Visualize looping |
| loopPlot-method | Visualize looping |
| loops | A class to represent ChIA-PET interaction data and annotations |
| loops-class | A class to represent ChIA-PET interaction data and annotations |
| loops.small | chr1:36000000-36300000 loops |
| loopsMake | Read preprocessed ChIA-PET data from dnaloop |
| loopsMake-method | Read preprocessed ChIA-PET data from dnaloop |
| loopsMake.mango | Read preprocessed ChIA-PET data from mango |
| loopsMake.mango-method | Read preprocessed ChIA-PET data from mango |
| loopsSubset | Subset two difloop objects |
| loopsSubset-method | Subset two difloop objects |
| loopWidth | Loop widths |
| loopWidth-method | Loop widths |
| mangoCorrection | Perform mango bias correction |
| mangoCorrection-method | Perform mango bias correction |
| manyLoopPlots | Plot several loop regions |
| manyLoopPlots-method | Plot several loop regions |
| mergeAnchors | Combine nearby anchors into one peak |
| mergeAnchors-method | Combine nearby anchors into one peak |
| numAnchors | Get number of anchors in each sample |
| numAnchors-method | Get number of anchors in each sample |
| numLoops | Per-sample loop quantities |
| numLoops-method | Per-sample loop quantities |
| padGRanges | Pad a GRanges object |
| padGRanges-method | Pad a GRanges object |
| pcaPlot | Visualize sample relationships |
| pcaPlot-method | Visualize sample relationships |
| plotTopLoops | Plot the most significant loops |
| plotTopLoops-method | Plot the most significant loops |
| quickAssoc | Perform quick differential loop calling |
| quickAssoc-method | Perform quick differential loop calling |
| quickAssocVoom | Perform quick differential loop calling |
| quickAssocVoom-method | Perform quick differential loop calling |
| removeRegion | Remove region from loops object |
| removeRegion-method | Remove region from loops object |
| removeSelfLoops | Remove self loops |
| removeSelfLoops-method | Remove self loops |
| rmchr | Remove 'chr' from GRanges seqnames |
| rmchr-method | Remove 'chr' from GRanges seqnames |
| sampleNames-method | Grab/Update Sample Names |
| sampleNames<--method | Grab/Update Sample Names |
| slidingWindowTest | Combined association test for all loops in a defined region |
| slidingWindowTest-method | Combined association test for all loops in a defined region |
| splitSamples | Split samples into their own loops object |
| splitSamples-method | Split samples into their own loops object |
| subsetLoops | Subset loops |
| subsetLoops-method | Subset loops |
| subsetRegion | Extract region from loops object |
| subsetRegion-method | Extract region from loops object |
| subsetRegionAB | Retain loops that have anchors in two specified regions |
| subsetRegionAB-method | Retain loops that have anchors in two specified regions |
| summary-method | Link the anchors and interactions back together |
| tail-method | Extract last part of loops object |
| topLoops | Grab top loops |
| topLoops-method | Grab top loops |
| union-method | Combine two loops objects |
| updateLDGroups | Update groups in colData for loops object |
| updateLDGroups-method | Update groups in colData for loops object |
| [-method | Extract parts of a loops object |