Showing : GenomicRanges • reset
7
votes
9
replies
345
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 11 days ago by 58k • written 15 days ago by ▴ 10
3
votes
5
replies
222
views
Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 5 weeks ago by 15k • written 5 weeks ago by • 0
4
votes
1
reply
144
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 9 weeks ago by 15k • written 9 weeks ago by ▴ 140
0
votes
3
replies
244
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 11 weeks ago by 58k • written 11 weeks ago by • 0
2
votes
4
replies
223
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 10 days ago by 15k • written 12 weeks ago by ▴ 10
0
votes
2
replies
184
views
Handling missing seqlenghts
GenomicRanges
12 weeks ago Charles Plessy ▴ 140
4
votes
2
replies
262
views
GenomicRanges::union fails on R devel
devel GenomicRanges
3 months ago Guillaume Devailly ▴ 40
5
votes
2
replies
289
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4 months ago Pratik Mehta ▴ 10
2
votes
2
replies
241
views
How to subset GRangesList by seqnames
GenomicRanges
updated 4 months ago by 58k • written 4 months ago by ▴ 10
1
vote
2
replies
277
views
`GenomicRanges` cheat sheet
GenomicRanges
4 months ago chirag.parsania • 0
0
votes
2
replies
251
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
4 months ago Arslan • 0
0
votes
2
replies
173
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
5 months ago Daniel Cameron ▴ 20
2
votes
4
replies
398
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
5 months ago • updated 4 months ago maltethodberg ▴ 140
0
votes
1
reply
147
views
How to overlap granges objects by gene name
GenomicRanges
updated 6 months ago by 58k • written 6 months ago by • 0
0
votes
5
replies
306
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
6 months ago rtrivedi1 ▴ 10
0
votes
0
replies
163
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
7 months ago Dario Strbenac ★ 1.5k
3
votes
2
replies
233
views
Should I create a new class or using Common Classes
GenomicRanges
updated 8 months ago by 15k • written 8 months ago by ▴ 20
0
votes
0
replies
164
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
8 months ago alorsonmethyle • 0
1
vote
4
replies
388
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
8 months ago Yixin • 0
11
votes
13
replies
988
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
14 months ago • updated 11 months ago rohitsatyam102 ▴ 20
1
vote
1
reply
385
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 12 months ago by 58k • written 12 months ago by • 0
1
vote
1
reply
266
views
Average coverage between multiple samples
GenomicRanges
updated 13 months ago by 11k • written 13 months ago by ▴ 90
14
votes
10
replies
11k
views
How do I merge a list of GRanges?
GenomicRanges
updated 11 months ago by ▴ 30 • written 5.6 years ago by ▴ 30
1
vote
1
reply
323
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 14 months ago by 58k • written 14 months ago by • 0
1
vote
3
replies
321
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
14 months ago rahnaman ▴ 10
2
votes
2
replies
466
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 14 months ago by 15k • written 16 months ago by ▴ 80
0
votes
0
replies
188
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
14 months ago Nala • 0
0
votes
0
replies
264
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
15 months ago r.a.policastro • 0
0
votes
1
reply
278
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 17 months ago by 58k • written 17 months ago by ▴ 50
3
votes
7
replies
549
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 17 months ago by 58k • written 17 months ago by ▴ 10
0
votes
0
replies
202
views
Expected Output for Promoters Used for GRangesList
GenomicRanges
18 months ago Dario Strbenac ★ 1.5k
0
votes
5
replies
340
views
GenomicRanges object no longer viewable
GenomicRanges
updated 19 months ago by 25k • written 19 months ago by ▴ 80
4
votes
2
replies
284
views
How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 20 months ago by 3.4k • written 20 months ago by • 0
0
votes
1
reply
250
views
Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
20 months ago Charles Plessy ▴ 140
0
votes
0
replies
272
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
21 months ago Guandong Shang ▴ 20
2
votes
2
replies
333
views
Genomic Ranges: Convert from 0-base to 1-base
GenomicRanges
updated 21 months ago by 11k • written 21 months ago by ▴ 10
1
vote
1
reply
523
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 21 months ago by 11k • written 21 months ago by ▴ 20
3
votes
4
replies
417
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 22 months ago by 15k • written 22 months ago by ▴ 20
0
votes
4
replies
819
views
Compilation error when attempting to install GenomicRanges from BiocManager.
software error GenomicRanges
22 months ago atheeth14 • 0
1
vote
1
reply
250
views
MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS RangedData GenomicRanges
updated 23 months ago by ▴ 570 • written 23 months ago by • 0
0
votes
6
replies
413
views
GenomicRanges: Find first, second and third nearest genes
R GenomicRanges Granges
updated 23 months ago by 44k • written 23 months ago by ▴ 20
0
votes
0
replies
264
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 23 months ago by 2.9k • written 23 months ago by • 0
3
votes
2
replies
316
views
GenomicRanges: Find N nearest/preceding/following ranges
genomicranges
updated 24 months ago by 11k • written 24 months ago by ▴ 140
6
votes
11
replies
3.3k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 24 months ago by • 0 • written 6.8 years ago by ▴ 20
2
votes
3
replies
264
views
GenomicFeatures promotersByOverlap: Identify promoters by overlap?
GenomicFeatures GenomicRanges
updated 2.0 years ago by 58k • written 2.0 years ago by ▴ 10
0
votes
3
replies
364
views
Resize exons in transcript to total width
genomicranges genomicfeatures
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 90
0
votes
1
reply
298
views
An error while finding pintersect()
GenomicRanges
2.2 years ago Prashantha Hebbar ▴ 260
0
votes
0
replies
262
views
SOLVED. finding distance to nearest neighbour (non-self) within a list in GenomicRanges
GenomicRanges GenomicFeatures grange distanceToNearest R
2.2 years ago rmash • 0
0
votes
1
reply
1.0k
views
Error in IRanges, In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"
Genomicranges IRanges
updated 2.3 years ago by 58k • written 2.3 years ago by • 0
2
votes
3
replies
481
views
Can GenomicRanges findOverlaps ignore seqnames?
GenomicRanges findOverlaps
2.3 years ago O. William McClung • 0
50 results • Page 1 of 1
Recent ...
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Comment: Need help for ProStaR Stand-alone install by benoit.marchand • 0
Thank you for answering. I've just updated to Prostar v1.26.3 and confirm that the **Prostar()** command **now works** in R for me on linu…
Answer: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Votes
Comment: Need help for ProStaR Stand-alone install
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
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