Ecosyste.ms: Issues

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GitHub / Bioconductor/GenomicRanges issues and pull requests

#84 - Add dummyfile.txt

Pull Request - State: closed - Opened by namhoangubs 6 months ago - 2 comments

#83 - subtract documentation

Issue - State: open - Opened by gevro 9 months ago - 6 comments

#82 - use empty strand when seqnames are also empty, closes #81

Pull Request - State: closed - Opened by LiNk-NY 11 months ago - 1 comment

#81 - Bug in makeGRangesFromDataFrame from empty data table

Issue - State: closed - Opened by gevro 12 months ago - 2 comments

#80 - is this an expected `gaps` behaviour?

Issue - State: closed - Opened by oleksii-nikolaienko 12 months ago - 7 comments

#79 - RleList subsetting has integer overflow on mammal genomes

Issue - State: open - Opened by alexfriman about 1 year ago

#78 - "object 'fancy_mseq' not found" when using "setdiff"

Issue - State: closed - Opened by Leo-ccc over 1 year ago - 5 comments

#77 - Could `GenomicRanges::binnedAverage()` be reused for other purposes?

Issue - State: open - Opened by ssayols over 1 year ago - 4 comments

#75 - Printing error with CompressedGRangesList

Issue - State: closed - Opened by llrs over 1 year ago - 3 comments

#74 - nearestKNeighbors does not handle seqlevel pruning

Issue - State: open - Opened by yeyuan98 over 1 year ago - 2 comments

#73 - Add `rworkflows` to test/document `GenomicRanges` in GitHub Actions

Pull Request - State: closed - Opened by bschilder almost 2 years ago - 27 comments

#72 - avoid duplicate chunk names in Ten_things_slides.Rnw

Pull Request - State: closed - Opened by LiNk-NY almost 2 years ago - 1 comment

#71 - drop.self and drop.redundant for Genomic Ranges

Issue - State: closed - Opened by DarioS almost 2 years ago - 3 comments

#70 - findOverlaps appears inconsistent

Issue - State: closed - Opened by cb4github almost 2 years ago - 4 comments

#69 - Convert ExtendingGenomicRanges.Rnw to .Rmd

Pull Request - State: open - Opened by hsadia538 almost 2 years ago - 7 comments

#68 - subtract for two GRangesList

Issue - State: closed - Opened by gevro about 2 years ago - 2 comments

#67 - setdiff not behaving as expected

Issue - State: open - Opened by gevro about 2 years ago

#66 - Representing missing ranges

Issue - State: open - Opened by LiNk-NY over 2 years ago

#65 - In v1.46.1 seqnames changed when added to GRangesList

Issue - State: closed - Opened by peterch405 over 2 years ago - 9 comments

#64 - Annotate each range in a Granges object with a vector

Issue - State: closed - Opened by gevro over 2 years ago - 1 comment

#63 - Strange integer overflow issue

Issue - State: closed - Opened by gevro over 2 years ago - 2 comments

#62 - Unexpected behavior of setdiff

Issue - State: closed - Opened by gevro over 2 years ago - 6 comments

#61 - Cannot unset strict.strand in intersect

Issue - State: closed - Opened by kewiechecki almost 3 years ago - 1 comment

#60 - Added a findOverlap method for character vectors.

Pull Request - State: open - Opened by LTLA about 3 years ago - 2 comments

#59 - add na.rm argument to makeGRangesFromDataFrame

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago - 5 comments

#58 - makeGRangesFromDataFrame check for missing cells before sending to IRanges

Issue - State: closed - Opened by liutiming over 3 years ago - 2 comments

#56 - problems with AtomicList in mcols in Rdevel

Issue - State: closed - Opened by plger over 3 years ago - 3 comments

#55 - findOverlaps is reporting overlaps that are not actual overlaps

Issue - State: closed - Opened by kac2053 over 3 years ago - 2 comments

#54 - Making seqinfo<- easier to use with new levels

Issue - State: closed - Opened by LTLA over 3 years ago - 16 comments

#53 - Document and export get_out_of_bound_index

Issue - State: open - Opened by rpolicastro over 3 years ago - 2 comments

#52 - overlaps with character arguments as seqlevels?

Issue - State: open - Opened by LTLA over 3 years ago

#50 - replace KEGG.db usage with KEGGREST and fix a makeGRangesFromDataFrame.Rd example

Pull Request - State: closed - Opened by vjcitn over 3 years ago - 3 comments

#49 - plan for dealing with loss of KEGG.db?

Issue - State: closed - Opened by vjcitn almost 4 years ago - 1 comment

#48 - Can't create GRanges Object with more than 11 peaks

Issue - State: closed - Opened by eonurk almost 4 years ago - 2 comments

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

Issue - State: open - Opened by PeteHaitch about 4 years ago - 2 comments

#44 - pc Performance Slow for Two GRangesList

Issue - State: open - Opened by DarioS about 4 years ago - 4 comments

#43 - Enhancement: Promoters Calculated Don't Overlap with Other Genes

Issue - State: open - Opened by DarioS about 4 years ago - 3 comments
Labels: enhancement

#42 - GenomicRanges::findKNN masks BiocNeighbors::findKNN

Issue - State: closed - Opened by LTLA about 4 years ago

#41 - Error in getListElement(x, i, ...)

Issue - State: closed - Opened by PeggySze over 4 years ago - 4 comments

#40 - Add FindKnn funcitonality

Pull Request - State: closed - Opened by dvantwisk over 4 years ago

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

Issue - State: closed - Opened by mdeber over 4 years ago - 5 comments

#38 - Integrate Felix's changes and add unit tests, closes #35

Pull Request - State: closed - Opened by LiNk-NY over 4 years ago

#37 - import error

Issue - State: closed - Opened by xuebaliang over 4 years ago - 2 comments

#36 - Errors attempting GenomicRanges:::findKNN()

Issue - State: closed - Opened by ShanSabri over 4 years ago - 3 comments

#35 - fixed makeGRangesFromDataFrame() for zero length DataFrame

Pull Request - State: closed - Opened by FelixErnst over 4 years ago - 1 comment

#34 - gpos/GPos equivalent for granges/GRanges

Issue - State: closed - Opened by MalteThodberg over 4 years ago - 2 comments

#33 - strange code for GenomicRanges:::compatibleStrand

Issue - State: open - Opened by msannell over 4 years ago - 1 comment

#32 - expand makeGRangesFromDataFrame functionality

Pull Request - State: open - Opened by LiNk-NY over 4 years ago - 5 comments

#31 - no convenient SimpleGRangesList to CompressedGRangesList as function

Issue - State: closed - Opened by LiNk-NY almost 5 years ago - 2 comments

#30 - inner and outer mcols for GRangesFactor

Issue - State: open - Opened by LTLA over 5 years ago - 1 comment

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

Issue - State: closed - Opened by peterblattmann over 5 years ago - 1 comment

#28 - Specialize findOverlaps for GRangesFactor objects

Pull Request - State: open - Opened by LTLA over 5 years ago - 3 comments

#27 - Error in mapToTranscripts

Issue - State: closed - Opened by weir12 over 5 years ago - 2 comments

#26 - GRangesFactor should inherit from GenomicRanges

Issue - State: open - Opened by hpages over 5 years ago

#25 - Add GRangesFactor class

Issue - State: closed - Opened by hpages over 5 years ago - 10 comments

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

Issue - State: closed - Opened by hpages over 5 years ago - 1 comment

#23 - Feature request: make mcols on a GRangesList return a SplitDataFrameList

Issue - State: closed - Opened by FelixErnst over 5 years ago - 3 comments

#22 - Making it easier to convert from IGV coordinates

Issue - State: open - Opened by Roleren over 5 years ago

#21 - Export GenomicRanges object as gtf file

Issue - State: closed - Opened by roosheelpatel over 5 years ago - 1 comment

#19 - Bug in follow and precede

Issue - State: closed - Opened by LuukHenk almost 6 years ago - 1 comment

#17 - gaps and GRangesList

Issue - State: open - Opened by kasperdanielhansen almost 6 years ago - 3 comments

#16 - findOverlaps with type="equal" and a GRangesList

Issue - State: open - Opened by kasperdanielhansen almost 6 years ago - 6 comments

#15 - propagating names from RangesList to GRanges

Issue - State: closed - Opened by lawremi almost 6 years ago - 4 comments

#14 - Support distance() / nearest() for circular chromosomes

Issue - State: closed - Opened by vobencha almost 6 years ago - 2 comments

#13 - Feature request: GPos() constructor can make a GPos object from an IPos object

Issue - State: closed - Opened by hpages almost 6 years ago - 1 comment

#11 - Speed difference in way you add mcols to GRanges

Issue - State: closed - Opened by Roleren about 6 years ago - 4 comments

#10 - vignettes/GenomicRangesIntroduction.Rmd

Pull Request - State: closed - Opened by lwaldron about 6 years ago - 1 comment

#9 - GRangesList fails with named arguments

Issue - State: closed - Opened by LTLA over 6 years ago - 2 comments

#8 - Unit tests succeed but for the wrong reason

Issue - State: closed - Opened by mtmorgan over 6 years ago - 2 comments

#7 - 'update' methods need exporting?

Issue - State: closed - Opened by mtmorgan over 6 years ago - 1 comment

#6 - Easy access to inner metadata of a GRangesList

Issue - State: open - Opened by LTLA over 6 years ago - 7 comments

#5 - Fix typos in intra-range-methods.Rd

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 1 comment

#4 - IRanges promoters changes coming to GenomicRanges?

Issue - State: closed - Opened by PeteHaitch over 6 years ago - 2 comments

#3 - Equisplit

Pull Request - State: closed - Opened by alexandremkuhn over 6 years ago - 9 comments

#2 - Sorting a SortedByQueryHits produces a Hits

Issue - State: closed - Opened by LTLA almost 7 years ago - 1 comment

#1 - Some fixes I would like

Issue - State: closed - Opened by Roleren almost 7 years ago - 1 comment