Showing : GenomicRanges • reset
0
votes
0
replies
95
views
Finding duplicated entries in GRangesList
GenomicRanges
5 weeks ago Marco • 0
1
vote
4
replies
1.9k
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges tidySummarizedExperiment tidyomics
5 months ago • updated 14 days ago Kateřina • 0
4
votes
2
replies
1.3k
views
GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
4 months ago pineiroalejandro ▴ 10
0
votes
0
replies
402
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
5 months ago jamiecatalano2 • 0
1
vote
4
replies
1.0k
views
fast apply on RleList
GenomicRanges RleList
5 months ago story.benjamin ▴ 20
2
votes
1
reply
1.0k
views
Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges CNEr
5 months ago 1324087964 • 0
0
votes
1
reply
1.2k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 7 months ago by 43k • written 4.4 years ago by • 0
1
vote
1
reply
1.9k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 7 months ago by 43k • written 5.0 years ago by • 0
0
votes
0
replies
380
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
11 months ago info ▴ 10
3
votes
3
replies
755
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
12 months ago • updated 9 months ago mat149 ▴ 80
0
votes
0
replies
483
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
13 months ago user_bioinfo • 0
2
votes
1
reply
570
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 17 months ago by 43k • written 17 months ago by ▴ 80
0
votes
0
replies
636
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
18 months ago gshweta95 • 0
0
votes
0
replies
617
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
19 months ago mat149 ▴ 80
2
votes
1
reply
820
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
20 months ago mat149 ▴ 80
0
votes
2
replies
1.3k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
3
votes
4
replies
1.8k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
0
votes
1
reply
1.1k
views
Error printing a CompressedGRangesList
GenomicRanges
2.7 years ago • updated 2.6 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
1.0k
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.7 years ago Delta._.43 ▴ 20
4
votes
4
replies
2.4k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.7 years ago by 68k • written 2.7 years ago by ★ 1.6k
3
votes
1
reply
1.1k
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.8 years ago by 43k • written 2.8 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 2.9 years ago by ★ 1.6k • written 2.9 years ago by • 0
2
votes
2
replies
3.2k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.0 years ago Mog • 0
0
votes
0
replies
879
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
3.2 years ago Simon Coetzee ▴ 50
2
votes
3
replies
3.1k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
3.3 years ago • updated 3.2 years ago Rodrigo • 0
0
votes
1
reply
1.6k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
3
votes
2
replies
2.1k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
3.4 years ago samantha.haque • 0
1
vote
2
replies
2.3k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.4 years ago vanbelj ▴ 30
0
votes
1
reply
1.6k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
1
vote
0
replies
1.2k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.5 years ago Charles Plessy ▴ 180
0
votes
2
replies
5.8k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.5 years ago by ▴ 20 • written 3.6 years ago by • 0
0
votes
6
replies
2.4k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.5 years ago by 68k • written 3.5 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
3.6 years ago svlachavas ▴ 840
6
votes
2
replies
1.8k
views
strand-aware GRanges shift
GenomicRanges
updated 3.7 years ago by ★ 1.6k • written 3.7 years ago by ▴ 10
9
votes
9
replies
5.0k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.7 years ago by 68k • written 3.7 years ago by ▴ 10
3
votes
5
replies
2.8k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.8 years ago by 16k • written 3.8 years ago by ▴ 40
4
votes
1
reply
1.1k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 180
1
vote
3
replies
7.9k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 10
2
votes
4
replies
4.6k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.7 years ago by 16k • written 3.9 years ago by ▴ 20
0
votes
2
replies
1.7k
views
Handling missing seqlenghts
GenomicRanges
3.9 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.6k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
4.0 years ago Guillaume Devailly ▴ 60
5
votes
2
replies
1.6k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.0 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.8k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 10
3
votes
2
replies
2.1k
views
`GenomicRanges` cheat sheet
GenomicRanges
4.1 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
4.1 years ago Arslan • 0
0
votes
2
replies
1.4k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
4.1 years ago Daniel Cameron ▴ 40
2
votes
4
replies
1.8k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
4.2 years ago • updated 4.0 years ago maltethodberg ▴ 180
0
votes
1
reply
988
views
How to overlap granges objects by gene name
GenomicRanges
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
5
replies
4.4k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.3 years ago rtrivedi1 ▴ 10
0
votes
0
replies
969
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
4.3 years ago Dario Strbenac ★ 1.6k
403 results • Page 1 of 9
Recent ...
Replies
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ReinholdGaylord99 • 0
Thank you so much! https://www.nature.com/articles/s41467-021-25960-2/ [geometry dash lite](https://geometrydashlite.online)
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising. Retaining …
Votes
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Awards • All
Popular Question to zhe ▴ 20
Popular Question to Natalia • 0
Popular Question to hauken_heyken ▴ 80
Scholar to Gordon Smyth 53k
Popular Question to Aaron Lun ★ 29k
Locations • All
United States, 46 minutes ago
The city by the bay, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 1521 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