Showing : Genomicranges • reset
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
5 weeks ago gshweta95 • 0
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199
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
11 weeks ago mat149 ▴ 70
2
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1
reply
264
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
3 months ago • updated 12 weeks ago mat149 ▴ 70
0
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2
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771
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 12 months ago by • 0 • written 12 months ago by • 0
3
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4
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935
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 13 months ago by 16k • written 14 months ago by • 0
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595
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
15 months ago Delta._.43 ▴ 20
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4
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1.2k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 15 months ago by 65k • written 15 months ago by ★ 1.5k
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1
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623
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Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
3
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1
reply
713
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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
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2
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1.1k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 18 months ago by ★ 1.6k • written 18 months ago by • 0
2
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2
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1.8k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
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0
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574
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago Simon Coetzee ▴ 50
2
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3
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1.7k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
22 months ago Rodrigo • 0
0
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1
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963
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 22 months ago by 65k • written 22 months ago by • 0
3
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2
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1.3k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
24 months ago samantha.haque • 0
1
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2
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1.5k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.0 years ago vanbelj ▴ 30
0
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1
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973
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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
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0
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780
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
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6
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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
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2
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3.7k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.1 years ago by ▴ 20 • written 2.2 years ago by • 0
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0
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693
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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
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2
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1.2k
views
strand-aware GRanges shift
GenomicRanges
updated 2.2 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
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9
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3.2k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
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5
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1.8k
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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
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1
reply
747
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 180
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3
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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
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4
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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
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2
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1.0k
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Handling missing seqlenghts
GenomicRanges
2.5 years ago Charles Plessy ▴ 180
4
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2
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1.2k
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GenomicRanges::union fails on R devel
devel GenomicRanges
2.6 years ago Guillaume Devailly ▴ 60
5
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2
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1.1k
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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
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2
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1.2k
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How to subset GRangesList by seqnames
GenomicRanges
updated 2.6 years ago by 65k • written 2.7 years ago by ▴ 10
2
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2
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1.3k
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`GenomicRanges` cheat sheet
GenomicRanges
2.7 years ago chirag.parsania • 0
0
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2
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1.1k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.7 years ago Arslan • 0
0
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2
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949
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GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.7 years ago Daniel Cameron ▴ 40
2
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4
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1.2k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.8 years ago • updated 2.6 years ago maltethodberg ▴ 180
0
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1
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623
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How to overlap granges objects by gene name
GenomicRanges
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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5
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2.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.8 years ago rtrivedi1 ▴ 10
0
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0
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669
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago Dario Strbenac ★ 1.5k
3
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2
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787
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Should I create a new class or using Common Classes
GenomicRanges
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 40
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0
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716
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.0 years ago alorsonmethyle • 0
1
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4
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1.5k
views
IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.0 years ago Yixin • 0
1
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1
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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
898
views
Average coverage between multiple samples
GenomicRanges
updated 3.4 years ago by ★ 11k • written 3.4 years ago by ▴ 90
11
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13
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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
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1
reply
1.2k
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GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
1
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3
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1.9k
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Merging Neighboring Genomic Segments
Granges GenomicRanges
3.5 years ago rahnaman ▴ 10
0
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0
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835
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annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
3.5 years ago Nala • 0
0
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0
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1.2k
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
3.6 years ago r.a.policastro • 0
2
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2
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1.5k
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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
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1
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1.1k
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How can i get repetitive elements genomic ranges in human genome?
repetitive elements IRanges GenomicRanges BSgenome
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 50
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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