Man pages for aryeelab/diffloop
Identifying differential DNA loops from chromatin topology data
| addchr | Add 'chr' to GRanges seqnames |
| annotateAnchors | Add meta data column to anchors based on GRanges |
| annotateAnchors.bed | Add meta data column to anchors based on bedgraph scores |
| annotateAnchors.bigwig | Add meta data column to anchors based on .bigwig |
| annotateLoops | Annotate loops as Enhancer-Promoter or CTCF-CTCF |
| annotateLoops.dge | Annotate enhancer-promoter loops with differential gene... |
| bedToGRanges | Read a file and make a GRanges object |
| calcLDSizeFactors | Compute normalizing factors for each sample |
| callCCDs | Compute Chromatin Contact Domains (CCDs) |
| computeBoundaryScores | Compute boundary scores for genomic loci in between anchors |
| diffloop | diffloop: A package for differential DNA loop calling from... |
| dim-loops-method | See dimensions of loops object |
| featureTest | Combined association test for all loops in a defined region |
| filterLoops | Filter loops |
| filterSpanningLoops | Retain loops spanning some genomic feature |
| geneinfo | Human/mouse exon locations |
| getHumanGenes | Get protein coding gene regions |
| getHumanTSS | Get Human Transcription Start Sites |
| getMouseGenes | Get protein coding gene regions |
| getMouseTSS | Get Mouse Transcription Start Sites |
| head-loops-method | Extract first part of loops object |
| human.genes | Human protein coding genes |
| interchromosomal | Loops between chromosomes |
| intrachromosomal | Loops within chromosomes |
| keepCTCFloops | Keep CTCF loops |
| keepEPloops | Keep enhancer-promoter loops |
| loopAssoc | Generalized differential Loop Calling |
| loopDistancePlot | Visualize proportion of loops at distances |
| loopGenes | Determine genes contained within loops |
| loopMetrics | Types of loops |
| loopPlot | Visualize looping |
| loops-class | A class to represent ChIA-PET interaction data and... |
| loopsMake | Read preprocessed ChIA-PET data from dnaloop |
| loopsMake.mango | Read preprocessed ChIA-PET data from mango |
| loops.small | chr1:36000000-36300000 loops |
| loopsSubset | Subset two difloop objects |
| loopWidth | Loop widths |
| mangoCorrection | Perform mango bias correction |
| manyLoopPlots | Plot several loop regions |
| mergeAnchors | Combine nearby anchors into one peak |
| numAnchors | Get number of anchors in each sample |
| numLoops | Per-sample loop quantities |
| padGRanges | Pad a GRanges object |
| pcaPlot | Visualize sample relationships |
| plotTopLoops | Plot the most significant loops |
| quickAssoc | Perform quick differential loop calling |
| quickAssocVoom | Perform quick differential loop calling |
| removeRegion | Remove region from loops object |
| removeSelfLoops | Remove self loops |
| rmchr | Remove 'chr' from GRanges seqnames |
| sampleNames-loops-method | Grab/Update Sample Names |
| slidingWindowTest | Combined association test for all loops in a defined region |
| splitSamples | Split samples into their own loops object |
| sub-loops-numeric-numeric-missing-method | Extract parts of a loops object |
| subsetLoops | Subset loops |
| subsetRegion | Extract region from loops object |
| subsetRegionAB | Retain loops that have anchors in two specified regions |
| summary-loops-method | Link the anchors and interactions back together |
| tail-loops-method | Extract last part of loops object |
| topLoops | Grab top loops |
| union-loops-loops-method | Combine two loops objects |
| updateLDGroups | Update groups in colData for loops object |
