Bioconductor/GenomicRanges

Issues

• If invalid colum names are found when converting from `GRanges` to `data.frame` at least a warning should be printed

  #86 opened 2 months ago by lbeltrame
  2

• reduce documentation

  #85 opened 7 months ago by gevro
  2

• Could `GenomicRanges::binnedAverage()` be reused for other purposes?

  #77 opened 2 years ago by ssayols
  4

• subtract documentation

  #83 opened a year ago by gevro
  6

• Bug in makeGRangesFromDataFrame from empty data table

  #81 opened a year ago by gevro
  2

• is this an expected `gaps` behaviour?

  #80 opened a year ago by oleksii-nikolaienko
  7

• RleList subsetting has integer overflow on mammal genomes

  #79 opened a year ago by alexfriman
  0

• "object 'fancy_mseq' not found" when using "setdiff"

  #78 opened 2 years ago by Leo-ccc
  5

• Error in getListElement(x, i, ...) : GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment

  #76 opened 2 years ago by AntoniaChroni
  17

• Printing error with CompressedGRangesList

  #75 opened 2 years ago by llrs
  3

• nearestKNeighbors does not handle seqlevel pruning

  #74 opened 2 years ago by yeyuan98
  2

• drop.self and drop.redundant for Genomic Ranges

  #71 opened 2 years ago by DarioS
  3

• findOverlaps appears inconsistent

  #70 opened 2 years ago by cb4github
  4

• subtract for two GRangesList

  #68 opened 2 years ago by gevro
  2

• setdiff not behaving as expected

  #67 opened 2 years ago by gevro
  0

• Representing missing ranges

  #66 opened 3 years ago by LiNk-NY
  0

• In v1.46.1 seqnames changed when added to GRangesList

  #65 opened 3 years ago by peterch405
  9

• Annotate each range in a Granges object with a vector

  #64 opened 3 years ago by gevro
  1

• Strange integer overflow issue

  #63 opened 3 years ago by gevro
  2

• Unexpected behavior of setdiff

  #62 opened 3 years ago by gevro
  6

• Cannot unset strict.strand in intersect

  #61 opened 3 years ago by kewiechecki
  1

• problems with AtomicList in mcols in Rdevel

  #56 opened 4 years ago by plger
  3

• makeGRangesFromDataFrame check for missing cells before sending to IRanges

  #58 opened 4 years ago by liutiming
  2

• Could we directly save the metadata when we use the function makeTxDbFromGFF?

  #57 opened 4 years ago by Codezy99
  0

• findOverlaps is reporting overlaps that are not actual overlaps

  #55 opened 4 years ago by kac2053
  2

• Making seqinfo<- easier to use with new levels

  #54 opened 4 years ago by LTLA
  16

• plan for dealing with loss of KEGG.db?

  #49 opened 4 years ago by vjcitn
  1

• Document and export get_out_of_bound_index

  #53 opened 4 years ago by rpolicastro
  2

• overlaps with character arguments as seqlevels?

  #52 opened 4 years ago by LTLA
  0

• GRanges gives 'Error in getListElement' when creating objects

  #51 opened 4 years ago by zhezhenwang
  0

• Can't create GRanges Object with more than 11 peaks

  #48 opened 4 years ago by eonurk
  2

• GRanges Error: "Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent"

  #47 opened 4 years ago by ahorn720
  6

• GPos doesn't survive round-trip conversion to data.frame

  #46 opened 4 years ago by PeteHaitch
  2

• pc Performance Slow for Two GRangesList

  #44 opened 4 years ago by DarioS
  4

• Enhancement: Promoters Calculated Don't Overlap with Other Genes

  #43 opened 4 years ago by DarioS
  3

• numeric meta column collapsed for connecting ranges when converting from Rle to GRanges

  #45 opened 4 years ago by ruqianl
  1

• GenomicRanges::findKNN masks BiocNeighbors::findKNN

  #42 opened 4 years ago by LTLA
  0

• Error in getListElement(x, i, ...)

  #41 opened 5 years ago by PeggySze
  4

• Errors attempting GenomicRanges:::findKNN()

  #36 opened 5 years ago by ShanSabri
  3

• coverage() with small weight values returns non-zero values over empty positions

  #39 opened 5 years ago by mdeber
  5

• import error

  #37 opened 5 years ago by xuebaliang
  2

• gpos/GPos equivalent for granges/GRanges

  #34 opened 5 years ago by MalteThodberg
  2

• strange code for GenomicRanges:::compatibleStrand

  #33 opened 5 years ago by msannell
  1

• no convenient SimpleGRangesList to CompressedGRangesList as function

  #31 opened 5 years ago by LiNk-NY
  2

• inner and outer mcols for GRangesFactor

  #30 opened 5 years ago by LTLA
  1

• GRangesFactor should inherit from GenomicRanges

  #26 opened 5 years ago by hpages
  0

• GPos - Error in getClass(x) : “UnstitchedGPos” is not a defined class

  #29 opened 5 years ago by peterblattmann
  1

• Error in mapToTranscripts

  #27 opened 5 years ago by weir12
  2

• Add GRangesFactor class

  #25 opened 5 years ago by hpages
  10

• Inefficiency of GPos("chr1:1-4e8") with GenomicRanges 1.37.7

  #24 opened 6 years ago by hpages
  1