Showing : genomicranges • reset
0
votes
1
reply
1.0k
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 4 weeks ago by 43k • written 3.8 years ago by • 0
1
vote
1
reply
1.6k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 4 weeks ago by 43k • written 4.4 years ago by • 0
0
votes
0
replies
195
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
4 months ago info ▴ 10
3
votes
3
replies
506
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
5 months ago • updated 11 weeks ago mat149 ▴ 80
0
votes
0
replies
322
views
hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
6 months ago user_bioinfo • 0
2
votes
1
reply
431
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 10 months ago by 43k • written 10 months ago by ▴ 80
0
votes
0
replies
468
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
11 months ago gshweta95 • 0
0
votes
0
replies
486
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
12 months ago mat149 ▴ 80
2
votes
1
reply
664
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
13 months ago mat149 ▴ 80
0
votes
2
replies
1.1k
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 22 months ago by • 0 • written 22 months ago by • 0
3
votes
4
replies
1.5k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 24 months ago by 16k • written 24 months ago by • 0
0
votes
1
reply
937
views
Error printing a CompressedGRangesList
GenomicRanges
2.2 years ago • updated 2.0 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
902
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.1 years ago Delta._.43 ▴ 20
4
votes
4
replies
2.0k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.1 years ago by 68k • written 2.1 years ago by ★ 1.6k
3
votes
1
reply
975
views
Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.2 years ago by 43k • written 2.2 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 2.3 years ago by ★ 1.6k • written 2.3 years ago by • 0
2
votes
2
replies
2.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.4 years ago Mog • 0
0
votes
0
replies
775
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.7 years ago Simon Coetzee ▴ 50
2
votes
3
replies
2.7k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.7 years ago Rodrigo • 0
0
votes
1
reply
1.4k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
3
votes
2
replies
1.9k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
2.8 years ago samantha.haque • 0
1
vote
2
replies
2.1k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.9 years ago vanbelj ▴ 30
0
votes
1
reply
1.4k
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
1
vote
0
replies
1.0k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.9 years ago Charles Plessy ▴ 180
0
votes
2
replies
5.1k
views
Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.9 years ago by ▴ 20 • written 3.0 years ago by • 0
0
votes
6
replies
2.0k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.0 years ago by 68k • written 3.0 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
3.1 years ago svlachavas ▴ 840
6
votes
2
replies
1.6k
views
strand-aware GRanges shift
GenomicRanges
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by ▴ 10
9
votes
9
replies
4.4k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
3
votes
5
replies
2.4k
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.2 years ago by 16k • written 3.2 years ago by ▴ 40
4
votes
1
reply
983
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 180
1
vote
3
replies
7.2k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 10
2
votes
4
replies
4.1k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.2 years ago by 16k • written 3.4 years ago by ▴ 20
0
votes
2
replies
1.5k
views
Handling missing seqlenghts
GenomicRanges
3.4 years ago Charles Plessy ▴ 180
4
votes
2
replies
1.5k
views
GenomicRanges::union fails on R devel
devel GenomicRanges
3.4 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
3.5 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.6k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
3
votes
2
replies
1.8k
views
`GenomicRanges` cheat sheet
GenomicRanges
3.5 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
3.5 years ago Arslan • 0
0
votes
2
replies
1.2k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
3.6 years ago Daniel Cameron ▴ 40
2
votes
4
replies
1.6k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
3.6 years ago • updated 3.5 years ago maltethodberg ▴ 180
0
votes
1
reply
837
views
How to overlap granges objects by gene name
GenomicRanges
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
5
replies
3.9k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.7 years ago rtrivedi1 ▴ 10
0
votes
0
replies
852
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.7 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 3.8 years ago by 16k • written 3.8 years ago by ▴ 40
1
vote
4
replies
1.9k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.9 years ago • updated 3.8 years ago Yixin • 0
11
votes
13
replies
5.5k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.3 years ago • updated 4.1 years ago rohitsatyam102 ▴ 20
1
vote
1
reply
1.4k
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
1
vote
1
reply
1.2k
views
Average coverage between multiple samples
GenomicRanges
updated 4.2 years ago by ★ 11k • written 4.2 years ago by ▴ 90
20
votes
10
replies
21k
views
How do I merge a list of GRanges?
GenomicRanges
updated 3.1 years ago by ▴ 40 • written 8.7 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Answer: library org.Hs.eg.db failing to install by James W. MacDonald 68k
It should just install. ``` > library(BiocManager) Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14 ucrt) W…
Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0
Thank you so much for your quick reply! I was worried if some underlying technical artifact or unusual behavior would be causing the patter…
Answer: Surprising behavior for DEXseq dispersion estimate plot? by Michael Love 43k
The red points are just slowly moving toward -Inf. They tend to have variance < mean (if it were a simple design and you could just look at…
Answer: DESeq use in lipidomic analysis by Michael Love 43k
I would go for limma rather than a NB-based method. See the papers on limma for metabolomics / proteomics.
Answer: DiffBind - question on the use of filtered or unfiltered input data by robert • 0
[FFH4X][1] Injector is a Free Fire mod menu software that includes a variety of intriguing hack features such as aimbot, auto headshot, fly…
Votes
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Calculating TOM in blockwise WGCNA
A: What is the "linear model" part used for in Limma?
Awards • All
Popular Question to ramiro.barrantes ▴ 10
Popular Question to shepherl 4.1k
Teacher to Aaron Lun ★ 28k
Popular Question to Laurent Gatto 1.6k
Popular Question to JKim • 0
Locations • All
United States, 28 minutes ago
Mexico, 1 hour ago
Czechia, 2 hours ago
United States, 2 hours ago
United States, 2 hours ago
Traffic: 575 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