Showing : genomicranges • reset
0
votes
0
replies
120
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
2 days ago jamiecatalano2 • 0
0
votes
0
replies
45
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges tidySummarizedExperiment tidyomics
5 days ago Kateřina • 0
1
vote
4
replies
808
views
fast apply on RleList
GenomicRanges RleList
19 days ago • updated 18 days ago story.benjamin ▴ 20
2
votes
1
reply
859
views
Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges CNEr
21 days ago 1324087964 • 0
0
votes
1
reply
1.1k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 12 weeks ago by 43k • written 4.0 years ago by • 0
1
vote
1
reply
1.7k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 12 weeks ago by 43k • written 4.6 years ago by • 0
0
votes
0
replies
233
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
6 months ago info ▴ 10
3
votes
3
replies
569
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
7 months ago • updated 4 months ago mat149 ▴ 80
0
votes
0
replies
364
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
8 months ago user_bioinfo • 0
2
votes
1
reply
464
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 months ago by 43k • written 11 months ago by ▴ 80
0
votes
0
replies
507
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
13 months ago gshweta95 • 0
0
votes
0
replies
519
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
14 months ago mat149 ▴ 80
2
votes
1
reply
706
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
15 months ago • updated 14 months ago mat149 ▴ 80
0
votes
2
replies
1.2k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 24 months ago by • 0 • written 2.0 years ago by • 0
3
votes
4
replies
1.6k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.1 years ago by 16k • written 2.1 years ago by • 0
0
votes
1
reply
984
views
Error printing a CompressedGRangesList
GenomicRanges
2.3 years ago • updated 2.2 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
934
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.3 years ago Delta._.43 ▴ 20
4
votes
4
replies
2.2k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.3 years ago by 68k • written 2.3 years ago by ★ 1.6k
3
votes
1
reply
1.0k
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
2
replies
1.8k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
2
votes
2
replies
2.9k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.6 years ago Mog • 0
0
votes
0
replies
798
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.8 years ago Simon Coetzee ▴ 50
2
votes
3
replies
2.8k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.8 years ago Rodrigo • 0
0
votes
1
reply
1.5k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
3
votes
2
replies
2.0k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
3.0 years ago samantha.haque • 0
1
vote
2
replies
2.2k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.0 years ago vanbelj ▴ 30
0
votes
1
reply
1.5k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
1
vote
0
replies
1.1k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.0 years ago Charles Plessy ▴ 180
0
votes
2
replies
5.4k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.1 years ago by ▴ 20 • written 3.1 years ago by • 0
0
votes
6
replies
2.1k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
0
replies
1.0k
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
3.2 years ago svlachavas ▴ 840
6
votes
2
replies
1.6k
views
strand-aware GRanges shift
GenomicRanges
updated 3.2 years ago by ★ 1.6k • written 3.2 years ago by ▴ 10
9
votes
9
replies
4.7k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 10
3
votes
5
replies
2.5k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 40
4
votes
1
reply
1.0k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 180
1
vote
3
replies
7.6k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
2
votes
4
replies
4.3k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.3 years ago by 16k • written 3.5 years ago by ▴ 20
0
votes
2
replies
1.6k
views
Handling missing seqlenghts
GenomicRanges
3.5 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.5k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
3.6 years ago Guillaume Devailly ▴ 60
5
votes
2
replies
1.4k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.6 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.7k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 10
3
votes
2
replies
1.9k
views
`GenomicRanges` cheat sheet
GenomicRanges
3.6 years ago chirag.parsania ▴ 10
0
votes
2
replies
1.4k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
3.6 years ago Arslan • 0
0
votes
2
replies
1.3k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
3.7 years ago Daniel Cameron ▴ 40
2
votes
4
replies
1.6k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
3.8 years ago • updated 3.6 years ago maltethodberg ▴ 180
0
votes
1
reply
896
views
How to overlap granges objects by gene name
GenomicRanges
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
votes
5
replies
4.1k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.8 years ago rtrivedi1 ▴ 10
0
votes
0
replies
885
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.9 years ago Dario Strbenac ★ 1.6k
3
votes
2
replies
1.1k
views
Should I create a new class or using Common Classes
GenomicRanges
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 40
1
vote
4
replies
2.0k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
4.0 years ago Yixin • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Module membership vs gene significance result and Modules-trait relationships re by Vinaya • 0
Hi. I am having the same issue, and haven't found a solution still.
Comment: Feature Counts - potential bug with outfile.jcounts by Tom • 0
[Penistone Locksmith][1] I think that would be a great idea; a novel junction to annotated junction proximity output column. So if the nove…
Comment: Filtering after DESeq by caroline.zanchi • 0
I am going to try this right now, thanks !
Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to etiennedanis • 0
Popular Question to javier.ruizramirez • 0
Autobiographer to Paul Harrison ▴ 100
Locations • All
WEHI, Melbourne, Australia, 8 minutes ago
The city by the bay, 1 hour ago
Seattle, WA, United States, 2 hours ago
Germany, 3 hours ago
United States, 7 hours ago
Traffic: 716 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