Showing : GenomicRanges • reset
0
votes
1
reply
1.0k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 7 weeks ago by 43k • written 3.9 years ago by • 0
1
vote
1
reply
1.7k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 7 weeks ago by 43k • written 4.5 years ago by • 0
3
votes
3
replies
535
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
6 months ago • updated 3 months ago mat149 ▴ 80
0
votes
0
replies
210
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
4 months ago info ▴ 10
0
votes
0
replies
340
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
7 months ago user_bioinfo • 0
2
votes
1
reply
446
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 months ago by 43k • written 10 months ago by ▴ 80
0
votes
0
replies
482
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
12 months ago gshweta95 • 0
0
votes
0
replies
499
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
13 months ago mat149 ▴ 80
2
votes
1
reply
677
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
13 months ago mat149 ▴ 80
4
votes
5
replies
3.8k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 14 months ago by ▴ 10 • written 9.3 years ago by ▴ 10
0
votes
2
replies
1.1k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 23 months ago by • 0 • written 23 months ago by • 0
5
votes
6
replies
10k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 9.8 years ago by ▴ 140
3
votes
4
replies
1.6k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.0 years ago by 16k • written 2.0 years ago by • 0
0
votes
1
reply
953
views
Error printing a CompressedGRangesList
GenomicRanges
2.2 years ago • updated 2.1 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
910
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.2 years ago Delta._.43 ▴ 20
4
votes
4
replies
2.1k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.2 years ago by 68k • written 2.2 years ago by ★ 1.6k
3
votes
1
reply
993
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
2
replies
1.8k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 2.4 years ago by ★ 1.6k • written 2.4 years ago by • 0
2
votes
2
replies
2.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.5 years ago Mog • 0
8
votes
12
replies
6.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.7 years ago by • 0 • written 10.0 years ago by ▴ 20
2
votes
3
replies
2.7k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.7 years ago Rodrigo • 0
0
votes
0
replies
786
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.7 years ago Simon Coetzee ▴ 50
0
votes
1
reply
1.4k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
3
votes
2
replies
1.9k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
2.9 years ago samantha.haque • 0
1
vote
2
replies
2.1k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.9 years ago vanbelj ▴ 30
0
votes
1
reply
1.4k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
1
vote
0
replies
1.1k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.0 years ago Charles Plessy ▴ 180
0
votes
2
replies
5.2k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.0 years ago by ▴ 20 • written 3.0 years ago by • 0
15
votes
4
replies
12k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 3.0 years ago by 16k • written 8.8 years ago by ▴ 40
0
votes
6
replies
2.1k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
5
votes
8
replies
10k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.1 years ago by • 0 • written 9.5 years ago by ▴ 50
0
votes
0
replies
1.0k
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
3.1 years ago svlachavas ▴ 840
6
votes
2
replies
1.6k
views
strand-aware GRanges shift
GenomicRanges
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by ▴ 10
20
votes
10
replies
21k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3.1 years ago by ▴ 40 • written 8.8 years ago by ▴ 40
2
votes
4
replies
4.2k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.2 years ago by 16k • written 3.4 years ago by ▴ 20
9
votes
9
replies
4.5k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
3
votes
5
replies
2.5k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 40
0
votes
1
reply
1.6k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 3.3 years ago by • 0 • written 9.3 years ago by ▴ 10
4
votes
1
reply
997
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 180
1
vote
3
replies
7.3k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Handling missing seqlenghts
GenomicRanges
3.4 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.5k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
3.5 years ago Guillaume Devailly ▴ 60
2
votes
4
replies
1.6k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
3.7 years ago • updated 3.5 years ago maltethodberg ▴ 180
5
votes
2
replies
1.4k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.5 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.6k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
3
votes
2
replies
1.8k
views
`GenomicRanges` cheat sheet
GenomicRanges
3.5 years ago chirag.parsania ▴ 10
0
votes
2
replies
1.4k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
3.6 years ago • updated 3.5 years ago Arslan • 0
0
votes
2
replies
1.3k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
3.6 years ago Daniel Cameron ▴ 40
0
votes
1
reply
861
views
How to overlap granges objects by gene name
GenomicRanges
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
5
replies
4.0k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.7 years ago rtrivedi1 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
What is the cheapest day to fly on American Airlines? {Ask_Expert}
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to mdeea123 ▴ 10
Popular Question to GA ▴ 10
Popular Question to Elizabeth • 0
Popular Question to Kent • 0
Locations • All
Germany, 14 minutes ago
United Kingdom, 24 minutes ago
United Kingdom, 35 minutes ago
Germany/Heidelberg/German Cancer Research Center, 1 hour ago
EMBL Heidelberg, 1 hour ago
Traffic: 769 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6