Showing : Genomicranges • reset
1
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56
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 hours ago by 41k • written 12 hours ago by ▴ 70
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0
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124
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
6 weeks ago gshweta95 • 0
0
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0
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201
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
11 weeks ago mat149 ▴ 70
2
votes
1
reply
268
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
3 months ago mat149 ▴ 70
4
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5
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3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 3 months ago by ▴ 10 • written 8.4 years ago by ▴ 10
0
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2
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773
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 12 months ago by • 0 • written 12 months ago by • 0
5
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6
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9.4k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 9.0 years ago by ▴ 140
3
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4
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941
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 14 months ago by 16k • written 14 months ago by • 0
0
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1
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625
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
0
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0
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598
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
15 months ago Delta._.43 ▴ 20
4
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4
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1.2k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 15 months ago by 65k • written 15 months ago by ★ 1.5k
3
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1
reply
715
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 16 months ago by 41k • written 16 months ago by • 0
0
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2
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1.1k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 18 months ago by ★ 1.6k • written 18 months ago by • 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
8
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12
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5.5k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 21 months ago by • 0 • written 9.1 years ago by ▴ 20
2
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3
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1.7k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
22 months ago Rodrigo • 0
0
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0
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576
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago Simon Coetzee ▴ 50
0
votes
1
reply
966
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 22 months ago by 65k • written 22 months ago by • 0
3
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2
replies
1.3k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
24 months ago samantha.haque • 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.0 years ago vanbelj ▴ 30
0
votes
1
reply
976
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
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0
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781
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
0
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2
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3.7k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.2 years ago by • 0
15
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4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 2.1 years ago by 16k • written 7.9 years ago by ▴ 40
0
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6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
5
votes
8
replies
8.8k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 2.2 years ago by • 0 • written 8.6 years ago by ▴ 50
0
votes
0
replies
695
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.2 years ago svlachavas ▴ 830
6
votes
2
replies
1.2k
views
strand-aware GRanges shift
GenomicRanges
updated 2.3 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.3 years ago by ▴ 40 • written 7.9 years ago by ▴ 40
2
votes
4
replies
2.8k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.3 years ago by 16k • written 2.5 years ago by ▴ 20
9
votes
9
replies
3.2k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
3
votes
5
replies
1.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.4 years ago by 16k • written 2.4 years ago by ▴ 40
0
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1
reply
1.4k
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How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 2.5 years ago by • 0 • written 8.4 years ago by ▴ 10
4
votes
1
reply
751
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 180
0
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3
replies
5.2k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
0
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2
replies
1.1k
views
Handling missing seqlenghts
GenomicRanges
2.5 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.2k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
2.6 years ago Guillaume Devailly ▴ 60
2
votes
4
replies
1.2k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.8 years ago • updated 2.6 years ago maltethodberg ▴ 180
5
votes
2
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1.1k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.6 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.2k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 10
2
votes
2
replies
1.3k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.7 years ago chirag.parsania • 0
0
votes
2
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1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.7 years ago Arslan • 0
0
votes
2
replies
951
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.7 years ago Daniel Cameron ▴ 40
0
votes
1
reply
625
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
5
replies
2.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.9 years ago rtrivedi1 ▴ 10
7
votes
5
replies
1.8k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 6.0 years ago by ▴ 140
0
votes
0
replies
670
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago Dario Strbenac ★ 1.5k
3
votes
2
replies
790
views
Should I create a new class or using Common Classes
GenomicRanges
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 40
0
votes
1
reply
1.1k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 3.0 years ago by • 0 • written 5.0 years ago by • 0
1
vote
4
replies
1.5k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.0 years ago Yixin • 0
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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