Showing : GenomicRanges • reset
0
votes
0
replies
30
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
6 days ago Delta._.43 ▴ 20
4
votes
4
replies
133
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 8 days ago by 62k • written 10 days ago by ★ 1.5k
0
votes
0
replies
52
views
Error printing a CompressedGRangesList
GenomicRanges
23 days ago • updated 13 days ago Lluís Revilla Sancho ▴ 700
3
votes
1
reply
178
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 4 weeks ago by 39k • written 4 weeks ago by • 0
0
votes
2
replies
184
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 11 weeks ago by ★ 1.6k • written 11 weeks ago by • 0
2
votes
2
replies
315
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3 months ago Mog • 0
0
votes
0
replies
212
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
6 months ago Simon Coetzee ▴ 50
2
votes
3
replies
377
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
7 months ago • updated 6 months ago Rodrigo • 0
0
votes
1
reply
251
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 7 months ago by 62k • written 7 months ago by • 0
2
votes
2
replies
417
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
8 months ago samantha.haque • 0
1
vote
2
replies
446
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
9 months ago vanbelj ▴ 20
0
votes
1
reply
327
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 9 months ago by ▴ 530 • written 9 months ago by • 0
1
vote
0
replies
286
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
9 months ago Charles Plessy ▴ 170
0
votes
2
replies
1.3k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
6
replies
613
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 10 months ago by 62k • written 10 months ago by • 0
0
votes
0
replies
229
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
11 months ago svlachavas ▴ 800
6
votes
2
replies
583
views
strand-aware GRanges shift
GenomicRanges
updated 11 months ago by ★ 1.6k • written 11 months ago by ▴ 10
9
votes
9
replies
1.4k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 12 months ago by 62k • written 12 months ago by ▴ 10
3
votes
5
replies
876
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 13 months ago by 16k • written 13 months ago by ▴ 40
4
votes
1
reply
324
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 14 months ago by 16k • written 14 months ago by ▴ 170
0
votes
3
replies
1.9k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 14 months ago by 62k • written 15 months ago by • 0
2
votes
4
replies
1.1k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 12 months ago by 16k • written 15 months ago by ▴ 10
0
votes
2
replies
467
views
Handling missing seqlenghts
GenomicRanges
15 months ago Charles Plessy ▴ 170
4
votes
2
replies
593
views
GenomicRanges::union fails on R devel
devel GenomicRanges
16 months ago Guillaume Devailly ▴ 60
5
votes
2
replies
588
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
16 months ago Pratik Mehta ▴ 10
2
votes
2
replies
521
views
How to subset GRangesList by seqnames
GenomicRanges
updated 16 months ago by 62k • written 16 months ago by ▴ 10
2
votes
2
replies
667
views
`GenomicRanges` cheat sheet
GenomicRanges
16 months ago chirag.parsania • 0
0
votes
2
replies
532
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
16 months ago Arslan • 0
0
votes
2
replies
403
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
17 months ago Daniel Cameron ▴ 40
2
votes
4
replies
679
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
18 months ago • updated 16 months ago maltethodberg ▴ 140
0
votes
1
reply
302
views
How to overlap granges objects by gene name
GenomicRanges
updated 18 months ago by 62k • written 18 months ago by • 0
0
votes
5
replies
786
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
19 months ago rtrivedi1 ▴ 10
0
votes
0
replies
341
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
19 months ago Dario Strbenac ★ 1.5k
3
votes
2
replies
406
views
Should I create a new class or using Common Classes
GenomicRanges
updated 20 months ago by 16k • written 20 months ago by ▴ 40
0
votes
0
replies
329
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
21 months ago alorsonmethyle • 0
1
vote
4
replies
752
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
21 months ago • updated 20 months ago Yixin • 0
11
votes
13
replies
1.8k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
2.2 years ago • updated 24 months ago rohitsatyam102 ▴ 20
1
vote
1
reply
651
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 2.0 years ago by 62k • written 2.0 years ago by • 0
1
vote
1
reply
448
views
Average coverage between multiple samples
GenomicRanges
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 90
18
votes
10
replies
14k
views
How do I merge a list of GRanges?
GenomicRanges
updated 11 months ago by ▴ 40 • written 6.6 years ago by ▴ 30
1
vote
1
reply
651
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 2.2 years ago by 62k • written 2.2 years ago by • 0
1
vote
3
replies
595
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
2.2 years ago rahnaman ▴ 10
2
votes
2
replies
792
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 2.2 years ago by 16k • written 2.3 years ago by ▴ 80
0
votes
0
replies
373
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
2.2 years ago Nala • 0
0
votes
0
replies
572
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
2.3 years ago r.a.policastro • 0
0
votes
1
reply
500
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 2.4 years ago by 62k • written 2.4 years ago by ▴ 50
3
votes
7
replies
896
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 2.5 years ago by 62k • written 2.5 years ago by ▴ 20
0
votes
0
replies
364
views
Expected Output for Promoters Used for GRangesList
GenomicRanges
2.5 years ago Dario Strbenac ★ 1.5k
0
votes
5
replies
834
views
GenomicRanges object no longer viewable
GenomicRanges
updated 2.6 years ago by 25k • written 2.6 years ago by ▴ 80
5
votes
2
replies
795
views
How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 2.7 years ago by 3.7k • written 2.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Awards • All
Teacher to Michael Love 39k
Teacher to James W. MacDonald 62k
Popular Question to Assa Yeroslaviz ★ 1.5k
Scholar to ATpoint ★ 2.0k
Popular Question to adR ▴ 20
Locations • All
United States, 9 minutes ago
Australia, 14 minutes ago
India, 18 minutes ago
United States, 18 minutes ago
The city by the bay, 32 minutes ago
Traffic: 249 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