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Showing :
genomicranges
•
reset
0
votes
0
replies
116
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
5 weeks ago
gshweta95
• 0
0
votes
0
replies
198
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
10 weeks ago
mat149
▴ 70
2
votes
1
reply
262
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
3 months ago • updated 12 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 3 months ago by
russ.bainer
▴ 10 • written 8.4 years ago by
madsheilskov
▴ 10
0
votes
2
replies
770
views
GenomicRanges coult not be loaded after R upgrade
DESeq2
Bioconductor
GenomicRanges
updated 12 months ago by
Virginie
• 0 • written 12 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
931
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
619
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
594
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges
rtracklayer
15 months ago
Delta._.43
▴ 20
4
votes
4
replies
1.2k
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
710
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 18 months ago by
Malcolm Cook
★ 1.6k • written 18 months ago by
mike-zx
• 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik
Bioconductor
GenomicRanges
Biostrings
BSgenome
19 months ago
Mog
• 0
8
votes
12
replies
5.5k
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
22 months ago
Rodrigo
• 0
0
votes
0
replies
572
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago
Simon Coetzee
▴ 50
0
votes
1
reply
961
views
Can´t install GenomicRanges and rtracklayer
rtracklayer
GenomicRanges
Installation
updated 22 months ago by
James W. MacDonald
65k • written 22 months ago by
Johanna
• 0
3
votes
2
replies
1.3k
views
toGRanges help!
GenomicRanges
toGRanges
Bioconductor
24 months ago
samantha.haque
• 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges
rtracklayer
GenomicRanges
2.0 years ago
vanbelj
▴ 30
0
votes
1
reply
972
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings
GenomicRanges
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
MANYA_BIOINFO
• 0
1
vote
0
replies
779
views
How about a getSeq() method for GRanges ?
GenomicRanges
BSGenome
2.1 years ago
Charles Plessy
▴ 180
0
votes
2
replies
3.7k
views
Gene body coverage plot
plot
gene
GenomicRanges
Coverage
R
updated 2.1 years ago by
kent.riemondy
▴ 20 • written 2.2 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
8.8k
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
688
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 7.9 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
3.2k
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 2.4 years ago by
Hervé Pagès
16k • written 2.4 years ago by
jon.klonowski
▴ 40
0
votes
1
reply
1.4k
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
744
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by
Hervé Pagès
16k • written 2.5 years ago by
Charles Plessy
▴ 180
0
votes
3
replies
5.2k
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
2.8 years ago • updated 2.6 years ago
maltethodberg
▴ 180
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
1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter
GenomicRanges
rtracklayer
GRanges
2.7 years ago • updated 2.6 years ago
Arslan
• 0
0
votes
2
replies
948
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges
Genomic
2.7 years ago
Daniel Cameron
▴ 40
0
votes
1
reply
623
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
2.6k
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 6.0 years ago by
rcavalca
▴ 140
0
votes
0
replies
668
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago
Dario Strbenac
★ 1.5k
3
votes
2
replies
784
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 3.0 years ago by
Zender
• 0 • written 5.0 years ago by
bertb
• 0
1
vote
4
replies
1.5k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges
GenomicRanges
3.0 years ago
Yixin
• 0
0
votes
0
replies
714
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: Deseq2 and Normalization of RNA sequencing data
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kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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