R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

anchorlift | anchorlift |

dt2gr | Convert data.table to GRanges |

example_dnase | DNAaseI hypersensitivity sites for hg19A |

example_genes | RefSeq genes for hg19 |

gr2dt | Converts 'GRanges' to 'data.table' |

grbind | Concatenate 'GRanges', robust to different 'mcols' |

gr.breaks | gr.breaks |

gr.chr | Prepend "chr" to 'GRanges seqlevels' |

gr.collapse | Collapse adjacent ranges |

gr.dice | Dice up 'GRanges' into 'width = 1' 'GRanges' spanning the... |

gr.disjoin | GenomicRanges disjoin with some additional functionality |

gr.dist | Pairwise distance between two 'GRanges' |

gr.duplicated | Allows to restrict duplicates using "by" columns and allows... |

gr.end | Get the right ends of a 'GRanges' |

gr.findoverlaps | Wrapper to 'GenomicRanges::findOverlaps' with added... |

gr.fix | "Fixes" 'seqlengths' / 'seqlevels' |

gr.flatten | Lay ranges end-to-end onto a derivate "chromosome" |

gr.flipstrand | Flip strand on 'GRanges' |

grfo | Metadata join with coordinates as keys (wrapper to... |

grfo-shortcut | shortcut for gr.findoverlaps (strand-specific) |

gr.in | Versatile implementation of 'GenomicRanges::findOverlaps' |

gr.in-shortcut | subset x on y ranges while ignoring strand (strand-agnostic) |

gr.in-strand-shortcut | Subset x on y ranges, strand-specific |

grl1 | Fake rearrangement data (set 1) |

grl2 | Fake rearrangement data (set 2) |

grl.bind | Concatenate 'GRangesList' objects. |

grl.eval | Evaluate and aggregate expression on GRanges column in... |

grl.hiC | HiC data for chr14 from Lieberman-Aiden 2009 (in hg19),... |

grl.in | Check intersection of 'GRangesList' with windows on genome |

grl.pivot | Pivot a 'GRangesList', inverting "x" and "y" |

grl.reduce | grl.reduce |

grl.string | Create string representation of 'GRangesList' |

grl.unlist | Robust unlisting of 'GRangesList' that keeps track of origin |

gr.match | Alternative 'GenomicRanges::match' that accepts additional... |

gr.merge | merge GRanges by using coordinates as primary key |

gr.mid | Get the midpoints of 'GRanges' ranges |

gr.nochr | Remove chr prefix from GRanges seqlevels |

gr.nudge | Shift GRanges left |

gr.nudge-shortcut | Nudge GRanges right |

gr.pairflip | Create pairs of ranges and their strand-inverse |

gr.query | query ranges by applying an expression to ranges metadata |

gr.rand | Generate random 'GRanges' on genome |

gr.sample | Randomly sample 'GRanges' intervals within territory |

gr.setdiff | 'BiocGenerics::setdiff' shortcut (strand agnostic) |

gr.simplify | Calculates pairwise distance for rearrangements represented... |

gr.start | Get GRanges corresponding to beginning of range |

gr.string | Return UCSC style interval string corresponding to 'GRanges'... |

gr.stripstrand | gr.stripstrand |

gr.sub | Apply 'gsub' to seqlevels of a 'GRanges' |

gr.sum | gr.sum |

gr.tile | Tile ranges across 'GRanges' |

gr.tile.map | gr.tile.map |

gr.trim | Trims pile of 'GRanges' relative to the specified <local>... |

gr.val | Annotate 'GRanges' with values from another 'GRanges' |

gr.val-fractional | gr.val shortcut to get fractional overlap of gr1 by gr2,... |

gr.val-mean | gr.val shortcut to get mean values of subject "x" meta data... |

gr.val-numbers | gr.val shortcut to get total numbers of intervals in gr2... |

gr.val-O | gr.val shortcut to get fractional overlap of gr1 by gr2,... |

gr.val-shortcut | gr.val shortcut to get total numbers of intervals in gr2... |

gr.val-strand | gr.val shortcut to total per interval width of overlap of gr1... |

gr.val-total | gr.val shortcut to total per interval width of overlap of gr1... |

hg_seqlengths | Output standard human genome seqlengths |

parse.gr | parse.gr |

parse.grl | parse.grl |

ra.duplicated | ra.duplicated |

ra.overlaps | ra.overlaps |

rle.query | Queries an 'RleList' representing genomic data |

rrbind | Improved 'rbind' for intersecting/union columns of... |

seg2gr | Convert GRanges-like data.frame into GRanges |

si | 'Seqinfo' object for hg19 |

si2gr | Create 'GRanges' from 'Seqinfo' or 'BSgenome' |

standardize_segs | Takes and returns segs data frame standardized to a single... |

streduce | Reduce 'GRanges' and 'GRangesList' to miminal footprint |

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