Showing : Genomicranges • reset
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115
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
6 weeks ago Simon Coetzee ▴ 50
2
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3
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191
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
6 weeks ago Rodrigo • 0
0
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1
reply
103
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 6 weeks ago by 60k • written 6 weeks ago by • 0
2
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2
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175
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toGRanges help!
GenomicRanges toGRanges Bioconductor
3 months ago samantha.haque • 0
1
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2
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216
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3 months ago vanbelj ▴ 10
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1
reply
152
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 4 months ago by ▴ 390 • written 4 months ago by • 0
1
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0
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139
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
4 months ago Charles Plessy ▴ 170
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2
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667
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 4 months ago by • 0 • written 5 months ago by • 0
0
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6
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352
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 4 months ago by 60k • written 4 months ago by • 0
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0
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141
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
6 months ago svlachavas ▴ 800
5
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2
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388
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strand-aware GRanges shift
GenomicRanges
updated 6 months ago by ★ 1.6k • written 6 months ago by ▴ 10
9
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9
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867
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 7 months ago by 60k • written 7 months ago by ▴ 10
3
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5
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559
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 8 months ago by 15k • written 8 months ago by ▴ 40
4
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1
reply
245
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 9 months ago by 15k • written 9 months ago by ▴ 170
0
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3
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912
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Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 9 months ago by 60k • written 9 months ago by • 0
2
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4
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579
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 7 months ago by 15k • written 9 months ago by ▴ 10
0
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2
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320
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Handling missing seqlenghts
GenomicRanges
9 months ago Charles Plessy ▴ 170
4
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2
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432
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GenomicRanges::union fails on R devel
devel GenomicRanges
10 months ago Guillaume Devailly ▴ 40
5
votes
2
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429
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
11 months ago Pratik Mehta ▴ 10
2
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2
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372
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How to subset GRangesList by seqnames
GenomicRanges
updated 11 months ago by 60k • written 11 months ago by ▴ 10
2
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2
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476
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`GenomicRanges` cheat sheet
GenomicRanges
11 months ago chirag.parsania • 0
0
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2
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401
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
11 months ago Arslan • 0
0
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2
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291
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
12 months ago Daniel Cameron ▴ 40
2
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4
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534
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
12 months ago • updated 10 months ago maltethodberg ▴ 140
0
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1
reply
222
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How to overlap granges objects by gene name
GenomicRanges
updated 13 months ago by 60k • written 13 months ago by • 0
0
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5
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494
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
13 months ago rtrivedi1 ▴ 10
0
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0
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248
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
14 months ago Dario Strbenac ★ 1.5k
3
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2
replies
326
views
Should I create a new class or using Common Classes
GenomicRanges
updated 14 months ago by 15k • written 15 months ago by ▴ 20
0
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0
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238
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
15 months ago alorsonmethyle • 0
1
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4
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588
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
15 months ago Yixin • 0
11
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13
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1.3k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
20 months ago • updated 18 months ago rohitsatyam102 ▴ 20
1
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1
reply
546
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 19 months ago by 60k • written 19 months ago by • 0
1
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1
reply
349
views
Average coverage between multiple samples
GenomicRanges
updated 20 months ago by 11k • written 20 months ago by ▴ 90
18
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10
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13k
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How do I merge a list of GRanges?
GenomicRanges
updated 6 months ago by ▴ 40 • written 6.2 years ago by ▴ 30
1
vote
1
reply
503
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 21 months ago by 60k • written 21 months ago by • 0
1
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3
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419
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Merging Neighboring Genomic Segments
Granges GenomicRanges
21 months ago rahnaman ▴ 10
2
votes
2
replies
628
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges GenomeInfoDb BSgenome isCircular
updated 21 months ago by 15k • written 23 months ago by ▴ 80
0
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0
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284
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
21 months ago Nala • 0
0
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0
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413
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
22 months ago r.a.policastro • 0
0
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1
reply
389
views
How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 23 months ago by 60k • written 23 months ago by ▴ 50
3
votes
7
replies
774
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 2.0 years ago by 60k • written 2.0 years ago by ▴ 10
0
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0
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277
views
Expected Output for Promoters Used for GRangesList
GenomicRanges
2.0 years ago Dario Strbenac ★ 1.5k
0
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5
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620
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GenomicRanges object no longer viewable
GenomicRanges
updated 2.2 years ago by 25k • written 2.2 years ago by ▴ 80
4
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2
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463
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How to extract positions present in one genomic ranges object and not the other?
genomicranges r overlap
updated 2.3 years ago by 3.6k • written 2.3 years ago by • 0
0
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1
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346
views
Is there an easy way to do pos(x) <- pos(x) + 1 for a GPos object ?
GenomicRanges GPos
2.3 years ago Charles Plessy ▴ 170
0
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0
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400
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
2.3 years ago Guandong Shang ▴ 20
2
votes
2
replies
458
views
Genomic Ranges: Convert from 0-base to 1-base
GenomicRanges
updated 2.3 years ago by 11k • written 2.3 years ago by ▴ 10
1
vote
1
reply
867
views
Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
rtracklayer genomicranges granges
updated 2.3 years ago by 11k • written 2.4 years ago by ▴ 20
3
votes
4
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523
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how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 2.4 years ago by 15k • written 2.4 years ago by ▴ 20
0
votes
4
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1.3k
views
Compilation error when attempting to install GenomicRanges from BiocManager.
software error GenomicRanges
2.5 years ago atheeth14 • 0
50 results • Page 1 of 1
Recent ...
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Answer: Conversion of UniProt to Ensembl by James W. MacDonald 60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles by Fatemeh • 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles by James W. MacDonald 60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Comment: error running UniProt.ws by James W. MacDonald 60k
https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/UniProt.ws/nebbiolo1-install.html
Comment: error running UniProt.ws by James W. MacDonald 60k
@marcelramos You have introduced a dependency on `BiocBaseUtils`, but that package is only available in devel.
Votes
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
Answer: the difference between getGEO and getGEOSuppFiles
Answer: TPM normalization starting with read counts
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