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Showing :
GenomicRanges
•
reset
0
votes
0
replies
95
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
23 days ago
gshweta95
• 0
0
votes
0
replies
181
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
8 weeks ago
mat149
▴ 70
2
votes
1
reply
242
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
10 weeks ago
mat149
▴ 70
0
votes
2
replies
754
views
GenomicRanges coult not be loaded after R upgrade
DESeq2
Bioconductor
GenomicRanges
updated 11 months ago by
Virginie
• 0 • written 11 months ago by
gs12
• 0
3
votes
4
replies
887
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges
IRanges
updated 13 months ago by
Hervé Pagès
16k • written 13 months ago by
jbendik
• 0
0
votes
1
reply
595
views
Error printing a CompressedGRangesList
GenomicRanges
15 months ago • updated 13 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
565
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
15 months ago
Delta._.43
▴ 20
4
votes
4
replies
1.1k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Dario Strbenac
★ 1.5k
3
votes
1
reply
691
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges
GenomicRanges
updated 16 months ago by
Michael Love
41k • written 16 months ago by
d.s.h.andel-3
• 0
0
votes
2
replies
1.1k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 17 months ago by
Malcolm Cook
★ 1.6k • written 17 months ago by
mike-zx
• 0
2
votes
2
replies
1.7k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
18 months ago
Mog
• 0
0
votes
0
replies
562
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
21 months ago
Simon Coetzee
▴ 50
2
votes
3
replies
1.7k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges
plyranges
21 months ago
Rodrigo
• 0
0
votes
1
reply
930
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
Johanna
• 0
3
votes
2
replies
1.3k
views
toGRanges help!
GenomicRanges
toGRanges
Bioconductor
23 months ago
samantha.haque
• 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
24 months ago
vanbelj
▴ 30
0
votes
1
reply
945
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 2.0 years ago by
Basti
▴ 760 • written 2.0 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
766
views
How about a getSeq() method for GRanges ?
GenomicRanges
BSGenome
2.0 years ago
Charles Plessy
▴ 180
0
votes
2
replies
3.6k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 2.0 years ago by
kent.riemondy
▴ 20 • written 2.1 years ago by
svenbioinf
• 0
0
votes
6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges
methylKit
S4Vectors
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
hasche
• 0
0
votes
0
replies
666
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 2.2 years ago by
Malcolm Cook
★ 1.6k • written 2.2 years ago by
gene_bioconductor
▴ 10
9
votes
9
replies
3.1k
views
Subset GRanges by intersection
findOverlaps
GPos
GenomicRanges
subsetByOverlaps
updated 2.3 years ago by
James W. MacDonald
65k • written 2.3 years ago by
Robert
▴ 10
3
votes
5
replies
1.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges
split
chromosome
TxDb
updated 2.3 years ago by
Hervé Pagès
16k • written 2.3 years ago by
jon.klonowski
▴ 40
4
votes
1
reply
724
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
Charles Plessy
▴ 180
0
votes
3
replies
5.1k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges
genomicra
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Alexandre
• 0
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
Hervé Pagès
16k • written 2.5 years ago by
changxu.fan
▴ 20
0
votes
2
replies
1.0k
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
2.5 years ago
Guillaume Devailly
▴ 60
5
votes
2
replies
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 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Junghoon
▴ 10
2
votes
2
replies
1.3k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.6 years ago
chirag.parsania
• 0
0
votes
2
replies
1.0k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.6 years ago
Arslan
• 0
0
votes
2
replies
929
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges
Genomic
2.7 years ago
Daniel Cameron
▴ 40
2
votes
4
replies
1.2k
views
Unique GPos taking into account mcols
GenomicRanges
unique
GPos
2.7 years ago • updated 2.6 years ago
maltethodberg
▴ 170
0
votes
1
reply
611
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
grr4006
• 0
0
votes
5
replies
2.5k
views
Grange object subsetting using seqnames
Seqnames
makeGRangesFromDataFrame
GRanges
Subsetting
GenomicRanges
2.8 years ago
rtrivedi1
▴ 10
0
votes
0
replies
657
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.8 years ago
Dario Strbenac
★ 1.5k
3
votes
2
replies
767
views
Should I create a new class or using Common Classes
GenomicRanges
updated 2.9 years ago by
Hervé Pagès
16k • written 2.9 years ago by
Guandong Shang
▴ 40
0
votes
0
replies
701
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
3.0 years ago
alorsonmethyle
• 0
1
vote
4
replies
1.4k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges
GenomicRanges
3.0 years ago • updated 2.9 years ago
Yixin
• 0
11
votes
13
replies
3.9k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.4 years ago • updated 3.2 years ago
rohitsatyam102
▴ 20
1
vote
1
reply
1.1k
views
cannot create GRanges object anymore
GenomicR
GenomicRanges
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
zhezhen
• 0
1
vote
1
reply
873
views
Average coverage between multiple samples
GenomicRanges
updated 3.3 years ago by
Michael Lawrence
★ 11k • written 3.3 years ago by
Jake
▴ 90
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.2 years ago by
jon.klonowski
▴ 40 • written 7.8 years ago by
endrebak85
▴ 40
1
vote
1
reply
1.2k
views
GenomicRanges equivalent to bedtools cluster
IRanges
GenomicRanges
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
kalamari
• 0
1
vote
3
replies
1.8k
views
Merging Neighboring Genomic Segments
Granges
GenomicRanges
3.4 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 3.4 years ago by
Hervé Pagès
16k • written 3.6 years ago by
Chris Seidel
▴ 80
0
votes
0
replies
812
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr
GenomicRanges
3.5 years ago
Nala
• 0
0
votes
0
replies
1.2k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges
plyranges
3.5 years ago
r.a.policastro
• 0
50 results • Page
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by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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Chris
• 0
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Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
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Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
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ensembl to hgnc symbols creates duplicates
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