| anchorlift | anchorlift |
| append_by_field_from_seqnames | Appending by field in seqnames to metadata column |
| DIM | Always returns a length 2 vector describing dimensions of... |
| do.assign | Assign columns or list elements |
| 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' |
| grapes-times-grapes | x %*% y because it is an R primitive. |
| grbind | Concatenate 'GRanges', robust to different 'mcols' |
| gr.breaks | gr.breaks |
| gr.chr | Prepend "chr" to 'GRanges seqlevels' |
| gr.collapse | Collapse adjacent ranges |
| gr_construct_by | Adding on "by" field(s) to seqnames for more efficient by... |
| gr_deconstruct_by | Removing by field and random string barcode to seqnames for... |
| 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.fixseq | Get union of seqlengths from multiple GRanges-like objects |
| 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.end | Get the right ends of a 'GRangesList' |
| grl.eval | Evaluate and aggregate expression on GRanges column in... |
| grl.expand | grl.expand |
| grl.hiC | HiC data for chr14 from Lieberman-Aiden 2009 (in hg19),... |
| grl.in | Check intersection of 'GRangesList' with windows on genome |
| grl.in-shortcut | grl.in shortcut |
| grl.pivot | Pivot a 'GRangesList', inverting "x" and "y" |
| grl.query | query ranges by applying an expression to GRanges metadata... |
| grl.reduce | grl.reduce |
| grl.shrink | grl.shrink |
| grl.start | Get the left ends of a 'GRangesList' |
| 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.noval | get rid of mcols on GRanges/GRangesLists |
| gr.nudge | Shift GRanges left |
| gr.nudge-shortcut | Nudge GRanges right |
| gr.pairflip | Create pairs of ranges and their strand-inverse |
| gr.quantile | gr.quantile |
| gr.query | query ranges by applying an expression to ranges metadata |
| gr.rand | Generate random 'GRanges' on genome |
| gr.reduce | Minimal overlaps for GRanges/GRangesList |
| 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... |
| gUtils-package | gUtils - Extending GenomicRanges |
| hg_seqlengths | Output standard human genome seqlengths |
| MULTIDIM | Returns a length 2 vector describing first two dimensions of... |
| NCOL2 | Ensuring 2nd dimension of empty vector or NULL is 1 |
| parse.gr | parse.gr |
| parse.grl | parse.grl |
| ra.duplicated | ra.duplicated |
| ra.overlaps | ra.overlaps |
| rebin | reaggregate WGS bins around a new target value |
| rle.query | Queries an 'RleList' representing genomic data |
| rleseq | numbers up within repeating elements of a vector |
| 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 |
