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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
James W. MacDonald
62k • written 10 days ago by
Dario Strbenac
★ 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
Michael Love
39k • written 4 weeks ago by
d.s.h.andel-3
• 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
Malcolm Cook
★ 1.6k • written 11 weeks ago by
mike-zx
• 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
James W. MacDonald
62k • written 7 months ago by
Johanna
• 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
Basti
▴ 530 • written 9 months ago by
MANYA_BIOINFO
• 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
kent.riemondy
• 0 • written 10 months ago by
svenbioinf
• 0
0
votes
6
replies
613
views
Error: duplicate row.names
GenomicRanges
methylKit
S4Vectors
updated 10 months ago by
James W. MacDonald
62k • written 10 months ago by
hasche
• 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
Malcolm Cook
★ 1.6k • written 11 months ago by
gene_bioconductor
▴ 10
9
votes
9
replies
1.4k
views
Subset GRanges by intersection
findOverlaps
GPos
GenomicRanges
subsetByOverlaps
updated 12 months ago by
James W. MacDonald
62k • written 12 months ago by
Robert
▴ 10
3
votes
5
replies
876
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges
split
chromosome
TxDb
updated 13 months ago by
Hervé Pagès
16k • written 13 months ago by
jon.klonowski
▴ 40
4
votes
1
reply
324
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 14 months ago by
Hervé Pagès
16k • written 14 months ago by
Charles Plessy
▴ 170
0
votes
3
replies
1.9k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges
genomicra
updated 14 months ago by
James W. MacDonald
62k • written 15 months ago by
Alexandre
• 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
Hervé Pagès
16k • written 15 months ago by
changxu.fan
▴ 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
James W. MacDonald
62k • written 16 months ago by
Junghoon
▴ 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
James W. MacDonald
62k • written 18 months ago by
grr4006
• 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
Hervé Pagès
16k • written 20 months ago by
Guandong Shang
▴ 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
James W. MacDonald
62k • written 2.0 years ago by
zhezhen
• 0
1
vote
1
reply
448
views
Average coverage between multiple samples
GenomicRanges
updated 2.1 years ago by
Michael Lawrence
11k • written 2.1 years ago by
Jake
▴ 90
18
votes
10
replies
14k
views
How do I merge a list of GRanges?
GenomicRanges
updated 11 months ago by
jon.klonowski
▴ 40 • written 6.6 years ago by
endrebak85
▴ 30
1
vote
1
reply
651
views
GenomicRanges equivalent to bedtools cluster
IRanges
GenomicRanges
updated 2.2 years ago by
James W. MacDonald
62k • written 2.2 years ago by
kalamari
• 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
Hervé Pagès
16k • written 2.3 years ago by
Chris Seidel
▴ 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
James W. MacDonald
62k • written 2.4 years ago by
vinod.acear
▴ 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
James W. MacDonald
62k • written 2.5 years ago by
vanbelj
▴ 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
Martin Morgan
25k • written 2.6 years ago by
Chris Seidel
▴ 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
Kevin Blighe
3.7k • written 2.7 years ago by
Grinch
• 0
50 results • Page
1 of 1
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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
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