Showing : Genomicranges • reset
2
votes
1
reply
178
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 80
0
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0
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186
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
11 weeks ago gshweta95 • 0
0
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0
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242
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
3 months ago mat149 ▴ 80
2
votes
1
reply
332
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
4 months ago mat149 ▴ 80
0
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2
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807
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 13 months ago by • 0 • written 13 months ago by • 0
3
votes
4
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1.0k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 15 months ago by 16k • written 15 months ago by • 0
0
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1
reply
676
views
Error printing a CompressedGRangesList
GenomicRanges
17 months ago • updated 15 months ago Lluís Revilla Sancho ▴ 730
0
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0
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648
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
17 months ago Delta._.43 ▴ 20
4
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4
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1.3k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 17 months ago by 66k • written 17 months ago by ★ 1.5k
3
votes
1
reply
744
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 17 months ago by 42k • written 17 months ago by • 0
0
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2
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1.2k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 19 months ago by ★ 1.6k • written 19 months ago by • 0
2
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2
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1.9k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
20 months ago Mog • 0
0
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0
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600
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
23 months ago Simon Coetzee ▴ 50
2
votes
3
replies
1.9k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
23 months ago Rodrigo • 0
0
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1
reply
1.0k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 23 months ago by 66k • written 23 months ago by • 0
3
votes
2
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1.4k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
2.1 years ago samantha.haque • 0
1
vote
2
replies
1.6k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.1 years ago vanbelj ▴ 30
0
votes
1
reply
1.0k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
1
vote
0
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808
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.2 years ago Charles Plessy ▴ 180
0
votes
2
replies
3.9k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.2 years ago by ▴ 20 • written 2.3 years ago by • 0
0
votes
6
replies
1.6k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.2 years ago by 66k • written 2.2 years ago by • 0
0
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0
replies
751
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.3 years ago svlachavas ▴ 830
6
votes
2
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1.3k
views
strand-aware GRanges shift
GenomicRanges
updated 2.4 years ago by ★ 1.6k • written 2.4 years ago by ▴ 10
9
votes
9
replies
3.3k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.4 years ago by 66k • written 2.4 years ago by ▴ 10
3
votes
5
replies
1.9k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 40
4
votes
1
reply
799
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.6 years ago by 16k • written 2.6 years ago by ▴ 180
0
votes
3
replies
5.4k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 2.6 years ago by 66k • written 2.6 years ago by • 0
2
votes
4
replies
3.0k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.4 years ago by 16k • written 2.6 years ago by ▴ 20
0
votes
2
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1.1k
views
Handling missing seqlenghts
GenomicRanges
2.6 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.2k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
2.7 years ago Guillaume Devailly ▴ 60
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
2.8 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.3k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.8 years ago by 66k • written 2.8 years ago by ▴ 10
2
votes
2
replies
1.4k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.8 years ago chirag.parsania • 0
0
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2
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1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.8 years ago Arslan • 0
0
votes
2
replies
990
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.8 years ago Daniel Cameron ▴ 40
2
votes
4
replies
1.2k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.9 years ago • updated 2.7 years ago maltethodberg ▴ 180
0
votes
1
reply
643
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.9 years ago by 66k • written 2.9 years ago by • 0
0
votes
5
replies
2.8k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.0 years ago rtrivedi1 ▴ 10
0
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0
replies
690
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.0 years ago Dario Strbenac ★ 1.5k
3
votes
2
replies
847
views
Should I create a new class or using Common Classes
GenomicRanges
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 40
0
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0
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742
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.1 years ago alorsonmethyle • 0
1
vote
4
replies
1.5k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.1 years ago Yixin • 0
11
votes
13
replies
4.3k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.5 years ago • updated 3.4 years ago rohitsatyam102 ▴ 20
1
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1
reply
1.2k
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 3.4 years ago by 66k • written 3.4 years ago by • 0
1
vote
1
reply
950
views
Average coverage between multiple samples
GenomicRanges
updated 3.5 years ago by ★ 11k • written 3.5 years ago by ▴ 90
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.4 years ago by ▴ 40 • written 8.0 years ago by ▴ 40
1
vote
1
reply
1.3k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.6 years ago by 66k • written 3.6 years ago by • 0
1
vote
3
replies
2.0k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
3.6 years ago rahnaman ▴ 10
2
votes
2
replies
1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.6 years ago by 16k • written 3.7 years ago by ▴ 80
0
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0
replies
870
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
3.6 years ago Nala • 0
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
Votes
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
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