Showing : genomicranges • reset
0
votes
2
replies
403
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 4 months ago by • 0 • written 5 months ago by • 0
3
votes
4
replies
471
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 6 months ago by 16k • written 6 months ago by • 0
0
votes
1
reply
341
views
Error printing a CompressedGRangesList
GenomicRanges
8 months ago • updated 7 months ago Lluís Revilla Sancho ▴ 720
0
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0
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280
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
8 months ago Delta._.43 ▴ 20
4
votes
4
replies
589
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 8 months ago by 63k • written 8 months ago by ★ 1.5k
3
votes
1
reply
436
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 9 months ago by 40k • written 9 months ago by • 0
0
votes
2
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582
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 10 months ago by ★ 1.6k • written 10 months ago by • 0
2
votes
2
replies
926
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
11 months ago Mog • 0
0
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0
replies
380
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
14 months ago Simon Coetzee ▴ 50
2
votes
3
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1.1k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
14 months ago Rodrigo • 0
0
votes
1
reply
550
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 15 months ago by 63k • written 15 months ago by • 0
3
votes
2
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879
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toGRanges help!
GenomicRanges toGRanges Bioconductor
16 months ago samantha.haque • 0
1
vote
2
replies
1.0k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
17 months ago vanbelj ▴ 20
0
votes
1
reply
627
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 17 months ago by ▴ 720 • written 17 months ago by • 0
1
vote
0
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530
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
17 months ago Charles Plessy ▴ 180
0
votes
2
replies
2.7k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 18 months ago by • 0 • written 18 months ago by • 0
0
votes
6
replies
1.1k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 18 months ago by 63k • written 18 months ago by • 0
0
votes
0
replies
445
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
19 months ago svlachavas ▴ 810
6
votes
2
replies
881
views
strand-aware GRanges shift
GenomicRanges
updated 19 months ago by ★ 1.6k • written 19 months ago by ▴ 10
9
votes
9
replies
2.3k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 20 months ago by 63k • written 20 months ago by ▴ 10
3
votes
5
replies
1.4k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 21 months ago by 16k • written 21 months ago by ▴ 40
4
votes
1
reply
544
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 22 months ago by 16k • written 22 months ago by ▴ 180
0
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3
replies
3.7k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 22 months ago by 63k • written 23 months ago by • 0
2
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4
replies
2.0k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 20 months ago by 16k • written 23 months ago by ▴ 20
0
votes
2
replies
767
views
Handling missing seqlenghts
GenomicRanges
23 months ago Charles Plessy ▴ 180
4
votes
2
replies
923
views
GenomicRanges::union fails on R devel
devel GenomicRanges
24 months ago Guillaume Devailly ▴ 60
5
votes
2
replies
848
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.0 years ago Pratik Mehta ▴ 10
2
votes
2
replies
861
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.0 years ago by 63k • written 2.0 years ago by ▴ 10
2
votes
2
replies
990
views
`GenomicRanges` cheat sheet
GenomicRanges
2.0 years ago chirag.parsania • 0
0
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2
replies
762
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.0 years ago Arslan • 0
0
votes
2
replies
620
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.1 years ago Daniel Cameron ▴ 40
2
votes
4
replies
938
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.2 years ago • updated 24 months ago maltethodberg ▴ 170
0
votes
1
reply
459
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
0
votes
5
replies
1.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.2 years ago rtrivedi1 ▴ 10
0
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0
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493
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.3 years ago Dario Strbenac ★ 1.5k
3
votes
2
replies
557
views
Should I create a new class or using Common Classes
GenomicRanges
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 40
0
votes
0
replies
512
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
2.4 years ago alorsonmethyle • 0
1
vote
4
replies
1.1k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
2.4 years ago Yixin • 0
11
votes
13
replies
2.9k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
2.8 years ago • updated 2.6 years ago rohitsatyam102 ▴ 20
1
vote
1
reply
857
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 2.7 years ago by 63k • written 2.7 years ago by • 0
1
vote
1
reply
648
views
Average coverage between multiple samples
GenomicRanges
updated 2.8 years ago by 11k • written 2.8 years ago by ▴ 90
18
votes
10
replies
16k
views
How do I merge a list of GRanges?
GenomicRanges
updated 19 months ago by ▴ 40 • written 7.3 years ago by ▴ 30
1
vote
1
reply
930
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 2.8 years ago by 63k • written 2.8 years ago by • 0
1
vote
3
replies
1.2k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
2.8 years ago rahnaman ▴ 10
2
votes
2
replies
1.1k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 2.9 years ago by 16k • written 3.0 years ago by ▴ 80
0
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0
replies
595
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
2.9 years ago Nala • 0
0
votes
0
replies
895
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
3.0 years ago r.a.policastro • 0
0
votes
1
reply
734
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.1 years ago by 63k • written 3.1 years ago by ▴ 50
3
votes
7
replies
1.2k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.1 years ago by 63k • written 3.1 years ago by ▴ 20
0
votes
0
replies
553
views
Expected Output for Promoters Used for GRangesList
GenomicRanges
3.2 years ago Dario Strbenac ★ 1.5k
50 results • Page 1 of 1
Recent ...
Replies
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Answer: What MetaPhlAn3 database was used in cMD 3?
Comment: Speeding up of DelayedArray::write_block()
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