Bioconductor GenomicRanges issues

Bioconductor / GenomicRanges

Representation and manipulation of genomic intervals

https://bioconductor.org/packages/GenomicRanges

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issues

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reduce documentation

#85 gevro closed 4 months ago
2
Add dummyfile.txt

#84 namhoangubs closed 6 months ago
2
subtract documentation

#83 gevro opened 9 months ago
6
use empty strand when seqnames are also empty, closes #81

#82 LiNk-NY closed 11 months ago
1
Bug in makeGRangesFromDataFrame from empty data table

#81 gevro closed 11 months ago
2
is this an expected `gaps` behaviour?

#80 oleksii-nikolaienko closed 11 months ago
7
RleList subsetting has integer overflow on mammal genomes

#79 alexfriman opened 1 year ago
0
"object 'fancy_mseq' not found" when using "setdiff"

#78 Leo-ccc closed 1 year ago
5
Could `GenomicRanges::binnedAverage()` be reused for other purposes?

#77 ssayols opened 1 year ago
4
Error in getListElement(x, i, ...) : GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment

#76 AntoniaChroni opened 1 year ago
17
Printing error with CompressedGRangesList

#75 llrs closed 1 year ago
3
nearestKNeighbors does not handle seqlevel pruning

#74 yeyuan98 opened 1 year ago
2
Add `rworkflows` to test/document `GenomicRanges` in GitHub Actions

#73 bschilder closed 9 months ago
27
avoid duplicate chunk names in Ten_things_slides.Rnw

#72 LiNk-NY closed 1 year ago
1
drop.self and drop.redundant for Genomic Ranges

#71 DarioS closed 1 year ago
3
findOverlaps appears inconsistent

#70 cb4github closed 1 year ago
4
Convert ExtendingGenomicRanges.Rnw to .Rmd

#69 hsadia538 opened 1 year ago
7
subtract for two GRangesList

#68 gevro closed 2 years ago
2
setdiff not behaving as expected

#67 gevro opened 2 years ago
0
Representing missing ranges

#66 LiNk-NY opened 2 years ago
0
In v1.46.1 seqnames changed when added to GRangesList

#65 peterch405 closed 2 years ago
9
Annotate each range in a Granges object with a vector

#64 gevro closed 2 years ago
1
Strange integer overflow issue

#63 gevro closed 2 years ago
2
Unexpected behavior of setdiff

#62 gevro closed 2 years ago
6
Cannot unset strict.strand in intersect

#61 kewiechecki closed 2 years ago
1
Added a findOverlap method for character vectors.

#60 LTLA opened 3 years ago
2
add na.rm argument to makeGRangesFromDataFrame

#59 LiNk-NY closed 2 years ago
5
makeGRangesFromDataFrame check for missing cells before sending to IRanges

#58 liutiming closed 3 years ago
2
Could we directly save the metadata when we use the function makeTxDbFromGFF?

#57 Codezy99 opened 3 years ago
0
problems with AtomicList in mcols in Rdevel

#56 plger closed 3 years ago
3
findOverlaps is reporting overlaps that are not actual overlaps

#55 kac2053 closed 3 years ago
2
Making seqinfo<- easier to use with new levels

#54 LTLA closed 3 years ago
16
Document and export get_out_of_bound_index

#53 rpolicastro opened 3 years ago
2
overlaps with character arguments as seqlevels?

#52 LTLA opened 3 years ago
0
GRanges gives 'Error in getListElement' when creating objects

#51 zhezhenwang opened 3 years ago
0
replace KEGG.db usage with KEGGREST and fix a makeGRangesFromDataFrame.Rd example

#50 vjcitn closed 3 years ago
3
plan for dealing with loss of KEGG.db?

#49 vjcitn closed 3 years ago
1
Can't create GRanges Object with more than 11 peaks

#48 eonurk closed 3 years ago
2
GRanges Error: "Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent"

#47 ahorn720 closed 3 years ago
6
GPos doesn't survive round-trip conversion to data.frame

#46 PeteHaitch opened 4 years ago
2
numeric meta column collapsed for connecting ranges when converting from Rle to GRanges

#45 ruqianl closed 4 years ago
1
pc Performance Slow for Two GRangesList

#44 DarioS opened 4 years ago
4
Enhancement: Promoters Calculated Don't Overlap with Other Genes

#43 DarioS opened 4 years ago
3
GenomicRanges::findKNN masks BiocNeighbors::findKNN

#42 LTLA closed 4 years ago
0
Error in getListElement(x, i, ...)

#41 PeggySze closed 4 years ago
4
Add FindKnn funcitonality

#40 dvantwisk closed 4 years ago
0
coverage() with small weight values returns non-zero values over empty positions

#39 mdeber closed 4 years ago
5
Integrate Felix's changes and add unit tests, closes #35

#38 LiNk-NY closed 11 months ago
0
import error

#37 xuebaliang closed 4 years ago
2
Errors attempting GenomicRanges:::findKNN()

#36 ShanSabri closed 4 years ago
3