tidyomics plyranges issues

tidyomics / plyranges

A grammar of genomic data transformation

https://tidyomics.github.io/plyranges/

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issues

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[FEATURE REQUEST] mutate(across()) ?

#110 jayoung opened 4 months ago
0
group mutate revamp

#109 ppaxisa opened 5 months ago
15
speed up group_by operations with mutate

#108 ppaxisa closed 5 months ago
1
[FEATURE REQUEST] Join overlap by ranges as well as metadata

#107 shalvichirmade opened 7 months ago
0
[BUG] Inconsistent behaviour of join_nearest_downstream() with one unstranded range set?

#106 eggrandio opened 9 months ago
1
Adds `min.gapwidth` to `reduce_ranges`

#105 mikelove closed 5 months ago
0
Warning in package check: checking S3 generic/method consistency for `group_*`

#104 mikelove opened 9 months ago
0
[BUG] read_bed adds NA., NA.1 ... col names that then cannot be renamed by select

#103 ConYel closed 1 year ago
1
NSBS object error when trying to filter by overlap GRanges object from read_bam()

#102 mce13 opened 1 year ago
0
[BUG] reduce_ranges silently creates list columns and fails to do so so if nothing is reduced

#101 Nicolai-vKuegelgen opened 1 year ago
0
flip_strand() function?

#100 eggrandio opened 1 year ago
1
Selecting nonexistent columns prints confusing error message

#99 mschubert opened 1 year ago
0
remove mention of UCSC, as this has changed/not always applicable

#98 mikelove closed 9 months ago
0
Implements strandedness for filter_by_overlap() family. Closes #96.

#97 snystrom closed 5 months ago
1
[FEATURE REQUEST] implement strandedness for filter_by_overlap() family

#96 perinom closed 5 months ago
0
[feature request] add .drop argument to group_by, e.g. to include empty seqlevels

#95 jayoung opened 2 years ago
0
Feature request "pull" function

#94 eggrandio opened 2 years ago
3
add_nearest_distance not working

#93 u2058152 closed 2 years ago
4
[BUG] Unexpected result reduce_ranges

#92 ConYel opened 2 years ago
0
[BUG] Character List columns cause an error in join_overlap_left()

#91 smped opened 3 years ago
3
suggestion for anchor default text

#90 mikelove closed 3 years ago
1
[FEATURE REQUEST] Minimum overlap expressed as a percentage

#89 Alex-Nesta opened 3 years ago
0
[feature request] Import Blast tabular with comment lines

#88 ConYel opened 3 years ago
0
Question about usability

#87 tonperre closed 3 years ago
2
intersect_ranges vs join_overlap_intersect

#86 pawelqs closed 3 years ago
2
[BUG] stretch() not stretching $blocks in GRanges

#85 AngelCampos opened 3 years ago
6
[BUG] Add min.width argument for reduce_ranges

#84 whtns opened 4 years ago
4
Fix table in vignette

#83 PeteHaitch closed 4 years ago
1
Quick fix to join_nearest_distance docs

#82 snystrom closed 4 years ago
1
move to github actions

#81 sa-lee closed 4 years ago
0
Nearest distance helpers

#80 snystrom closed 4 years ago
8
distance to nearest helper function?

#79 snystrom closed 4 years ago
5
Issues loading a BAM file resulted from featurecounts

#78 ConYel closed 4 years ago
2
Computing KNN between two granges objects

#77 ShanSabri opened 4 years ago
2
Strange behaviour of join_nearest*

#76 smped closed 4 years ago
9
Feature: map_granges

#75 sa-lee opened 4 years ago
0
Refactor non-standard evaluation internals

#74 sa-lee opened 4 years ago
0
shift_downstream() doesn't work with vectors of same length as GenomicRanges object as the shift value

#73 Bostrolicious closed 4 years ago
4
Groupings

#72 sa-lee closed 4 years ago
0
left overlap join bug: seqinfo adds "."

#71 sa-lee closed 4 years ago
1
left joins fail on granges if right has no mcols and some left ranges do not overlap

#70 ripkrizbi closed 4 years ago
2
documentation error

#69 MattBrauer closed 4 years ago
1
Feature requeste for full join of GRanges

#68 alexyfyf opened 5 years ago
11
Performance issues with joining

#67 mschubert closed 5 years ago
1
Target GPos when computing coverage

#66 lawremi opened 5 years ago
1
adds slice method for Ranges

#65 sa-lee closed 4 years ago
0
feature request: add slice

#64 sa-lee closed 4 years ago
1
Should plyranges reexport tidyverse generics?

#63 sa-lee closed 5 years ago
7
as_granges doesn’t preserve S4 columns

#62 sa-lee closed 4 years ago
0
I think the conversion error may be coming from the IRanges package rather than plyranges here. I think this is due to there not being a `as.data.frame` method for IntegerRanges class. If we take the example from the IRanges constructor man page:

#61 iimog closed 5 years ago
1