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
0
votes
2
replies
770
views
GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 12 months ago by • 0 • written 12 months ago by • 0
3
votes
4
replies
931
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 13 months ago by 16k • written 13 months ago by • 0
0
votes
1
reply
618
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
593
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 65k • written 15 months ago by ★ 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 41k • written 16 months ago by • 0
0
votes
2
replies
1.1k
views
GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 17 months ago by ★ 1.6k • written 18 months ago by • 0
2
votes
2
replies
1.8k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
0
votes
0
replies
570
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago Simon Coetzee ▴ 50
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
1
reply
961
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 22 months ago by 65k • written 22 months ago by • 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
970
views
finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 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 ▴ 20 • written 2.2 years ago by • 0
0
votes
6
replies
1.5k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
0
votes
0
replies
687
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 ★ 1.6k • written 2.2 years ago by ▴ 10
9
votes
9
replies
3.2k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 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 16k • written 2.4 years ago by ▴ 40
4
votes
1
reply
744
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 180
0
votes
3
replies
5.2k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
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 16k • written 2.5 years ago by ▴ 20
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
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 65k • written 2.6 years ago by ▴ 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
946
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.7 years ago Daniel Cameron ▴ 40
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
0
votes
1
reply
622
views
How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
5
replies
2.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.8 years ago rtrivedi1 ▴ 10
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 16k • written 2.9 years ago by ▴ 40
0
votes
0
replies
714
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.0 years ago alorsonmethyle • 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
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.4 years ago • updated 3.3 years ago rohitsatyam102 ▴ 20
1
vote
1
reply
1.1k
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
1
vote
1
reply
894
views
Average coverage between multiple samples
GenomicRanges
updated 3.4 years ago by ★ 11k • written 3.4 years ago by ▴ 90
19
votes
10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.2 years ago by ▴ 40 • written 7.9 years ago by ▴ 40
1
vote
1
reply
1.2k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
vote
3
replies
1.9k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
3.5 years ago rahnaman ▴ 10
2
votes
2
replies
1.5k
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 3.5 years ago by 16k • written 3.6 years ago by ▴ 80
0
votes
0
replies
831
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
3.5 years ago Nala • 0
0
votes
0
replies
1.2k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
3.6 years ago r.a.policastro • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0 by James W. MacDonald 65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
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
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
United States, 5 minutes ago
European Union, 8 minutes ago
United States, 8 minutes ago
EMBL Heidelberg, 13 minutes ago
France, 14 minutes ago
Traffic: 801 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