Showing : genomicranges • reset
0
votes
0
replies
156
views
Finding duplicated entries in GRangesList
GenomicRanges
12 weeks ago Marco • 0
1
vote
4
replies
2.0k
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges tidySummarizedExperiment tidyomics
6 months ago • updated 8 weeks ago Kateřina • 0
4
votes
2
replies
1.3k
views
GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
6 months ago pineiroalejandro ▴ 10
0
votes
0
replies
439
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
6 months ago jamiecatalano2 • 0
1
vote
4
replies
1.1k
views
fast apply on RleList
GenomicRanges RleList
7 months ago story.benjamin ▴ 20
2
votes
1
reply
1.0k
views
Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges CNEr
7 months ago 1324087964 • 0
0
votes
1
reply
1.3k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 9 months ago by 43k • written 4.5 years ago by • 0
1
vote
1
reply
2.0k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 9 months ago by 43k • written 5.1 years ago by • 0
0
votes
0
replies
406
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
12 months ago info ▴ 10
3
votes
3
replies
806
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
13 months ago • updated 11 months ago mat149 ▴ 80
0
votes
0
replies
526
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
15 months ago user_bioinfo • 0
2
votes
1
reply
614
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 18 months ago by 43k • written 18 months ago by ▴ 80
0
votes
0
replies
762
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
19 months ago gshweta95 • 0
0
votes
0
replies
649
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
21 months ago mat149 ▴ 80
2
votes
1
reply
864
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
21 months ago mat149 ▴ 80
0
votes
2
replies
1.4k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.5 years ago by • 0 • written 2.6 years ago by • 0
3
votes
4
replies
1.8k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
Error printing a CompressedGRangesList
GenomicRanges
2.9 years ago • updated 2.7 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
1.1k
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.8 years ago Delta._.43 ▴ 20
4
votes
4
replies
2.5k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.8 years ago by 68k • written 2.8 years ago by ★ 1.6k
3
votes
1
reply
1.2k
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
2
replies
2.0k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 3.0 years ago by ★ 1.6k • written 3.0 years ago by • 0
2
votes
2
replies
3.3k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.1 years ago Mog • 0
0
votes
0
replies
917
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
3.4 years ago Simon Coetzee ▴ 50
2
votes
3
replies
3.1k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
3.4 years ago Rodrigo • 0
0
votes
1
reply
1.7k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
3
votes
2
replies
2.2k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
3.5 years ago samantha.haque • 0
1
vote
2
replies
2.4k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.6 years ago vanbelj ▴ 30
0
votes
1
reply
1.7k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
1
vote
0
replies
1.2k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.6 years ago Charles Plessy ▴ 180
0
votes
2
replies
6.0k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.6 years ago by ▴ 20 • written 3.7 years ago by • 0
0
votes
6
replies
2.5k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
votes
0
replies
1.2k
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
3.8 years ago svlachavas ▴ 840
6
votes
2
replies
1.8k
views
strand-aware GRanges shift
GenomicRanges
updated 3.8 years ago by ★ 1.6k • written 3.8 years ago by ▴ 10
9
votes
9
replies
5.1k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.8 years ago by 68k • written 3.9 years ago by ▴ 10
3
votes
5
replies
2.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 40
4
votes
1
reply
1.2k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 180
1
vote
3
replies
8.0k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 10
2
votes
4
replies
4.6k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.8 years ago by 16k • written 4.0 years ago by ▴ 20
0
votes
2
replies
1.8k
views
Handling missing seqlenghts
GenomicRanges
4.1 years ago • updated 4.0 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.7k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
4.1 years ago Guillaume Devailly ▴ 60
5
votes
2
replies
1.7k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.2 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.9k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 10
3
votes
2
replies
2.1k
views
`GenomicRanges` cheat sheet
GenomicRanges
4.2 years ago chirag.parsania ▴ 10
0
votes
2
replies
1.5k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
4.2 years ago Arslan • 0
0
votes
2
replies
1.4k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
4.3 years ago Daniel Cameron ▴ 40
2
votes
4
replies
1.9k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
4.3 years ago • updated 4.1 years ago maltethodberg ▴ 180
0
votes
1
reply
1.0k
views
How to overlap granges objects by gene name
GenomicRanges
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
5
replies
4.5k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.4 years ago rtrivedi1 ▴ 10
0
votes
0
replies
995
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
4.4 years ago Dario Strbenac ★ 1.6k
403 results • Page 1 of 9
Recent ...
Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Stephen Piccolo ▴ 600
Popular Question to Maria Doyle ▴ 100
Popular Question to Hervé Pagès 16k
Popular Question to shepherl 4.2k
Locations • All
WEHI, Melbourne, Australia, 28 minutes ago
Germany, 1 hour ago
Russia, 3 hours ago
United States, 5 hours ago
Barcelona, Spain, 6 hours ago
Traffic: 1101 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