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Showing :
GenomicRanges
•
reset
0
votes
0
replies
97
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
25 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
244
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
11 weeks ago • updated 10 weeks ago
mat149
▴ 70
4
votes
5
replies
3.2k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges
genomicfeatures
translation
updated 12 weeks ago by
russ.bainer
▴ 10 • written 8.4 years ago by
madsheilskov
▴ 10
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
5
votes
6
replies
9.3k
views
Merge multiple genomic intervals if overlapping more than xx percents
genomicranges
written 8.9 years ago by
samuel collombet
▴ 140
3
votes
4
replies
892
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
596
views
Error printing a CompressedGRangesList
GenomicRanges
15 months ago • updated 13 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
566
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
693
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
8
votes
12
replies
5.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges
genomicfeatures
iranges
updated 21 months ago by
mehdi
• 0 • written 9.1 years ago by
cookie
▴ 20
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
0
replies
562
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
21 months ago
Simon Coetzee
▴ 50
0
votes
1
reply
933
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
948
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 2.0 years ago by
Basti
▴ 770 • 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 2.1 years ago by
kent.riemondy
▴ 20 • written 2.1 years ago by
svenbioinf
• 0
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges
grangeslist
granges
s4
updated 2.1 years ago by
Hervé Pagès
16k • written 7.9 years ago by
richierocks
▴ 40
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
5
votes
8
replies
8.7k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges
genomicranges
iranges
subsetByOverlaps
updated 2.2 years ago by
b.simpson
• 0 • written 8.6 years ago by
vinod.acear
▴ 50
0
votes
0
replies
667
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
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
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
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
0
votes
1
reply
1.3k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures
genomicranges
cds
overlap
updated 2.4 years ago by
balajee
• 0 • written 8.4 years ago by
madsheilskov
▴ 10
4
votes
1
reply
725
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
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
2.6 years ago
Guillaume Devailly
▴ 60
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
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
931
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges
Genomic
2.7 years ago
Daniel Cameron
▴ 40
0
votes
1
reply
612
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
7
votes
5
replies
1.8k
views
Strange error in bsseq when trying to assign seqinfo
bsseq
genomeinfodb
genomicranges
seqinfo
written 5.9 years ago by
rcavalca
▴ 140
0
votes
0
replies
659
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.8 years ago
Dario Strbenac
★ 1.5k
3
votes
2
replies
768
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
1
reply
1.1k
views
Unable to annotate in ChIPQC using yeast genome
ChIPQC
GenomicRanges
ChIPpeakAnno
updated 2.9 years ago by
Zender
• 0 • written 4.9 years ago by
bertb
• 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
0
votes
0
replies
703
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges
GenomicRanges
3.0 years ago
alorsonmethyle
• 0
50 results • Page
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Recent ...
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Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up question. Following up in In your [1-2-3 article][1], you say that > "... the …
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Comment: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
Or that. ;-D
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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