Showing : GenomicRanges • reset
2
votes
1
reply
146
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 13 days ago by 42k • written 13 days ago by ▴ 70
0
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0
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141
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
7 weeks ago gshweta95 • 0
0
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0
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212
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
3 months ago mat149 ▴ 70
2
votes
1
reply
294
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
3 months ago mat149 ▴ 70
0
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2
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789
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
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4
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965
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 14 months ago by 16k • written 14 months ago by • 0
0
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1
reply
644
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
0
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0
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612
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
16 months ago Delta._.43 ▴ 20
4
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4
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1.2k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 16 months ago by 65k • written 16 months ago by ★ 1.5k
3
votes
1
reply
724
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 17 months ago by 42k • written 17 months ago by • 0
0
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2
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1.2k
views
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
votes
2
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1.9k
views
getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
19 months ago Mog • 0
0
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0
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586
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
22 months ago Simon Coetzee ▴ 50
2
votes
3
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1.8k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
22 months ago Rodrigo • 0
0
votes
1
reply
987
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 23 months ago by 65k • written 23 months ago by • 0
3
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2
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1.3k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
2.0 years ago samantha.haque • 0
1
vote
2
replies
1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.1 years ago vanbelj ▴ 30
0
votes
1
reply
987
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
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795
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
0
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2
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3.8k
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 2.2 years ago by 65k • written 2.2 years ago by • 0
0
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0
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717
views
Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.3 years ago svlachavas ▴ 830
6
votes
2
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1.2k
views
strand-aware GRanges shift
GenomicRanges
updated 2.3 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
9
votes
9
replies
3.2k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.4 years ago by 65k • written 2.4 years ago by ▴ 10
3
votes
5
replies
1.9k
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
768
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
2.9k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.4 years ago by 16k • written 2.6 years ago by ▴ 20
0
votes
2
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1.1k
views
Handling missing seqlenghts
GenomicRanges
2.6 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
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1.1k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
2.7 years ago Pratik Mehta ▴ 10
2
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2
replies
1.2k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 10
2
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2
replies
1.4k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.7 years ago chirag.parsania • 0
0
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2
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1.1k
views
Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.7 years ago Arslan • 0
0
votes
2
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962
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.8 years ago Daniel Cameron ▴ 40
2
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4
replies
1.2k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
2.8 years ago • updated 2.7 years ago maltethodberg ▴ 180
0
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1
reply
632
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
2.7k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.9 years ago rtrivedi1 ▴ 10
0
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0
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679
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago Dario Strbenac ★ 1.5k
3
votes
2
replies
813
views
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
0
votes
0
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729
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
3.1 years ago • updated 3.0 years ago Yixin • 0
11
votes
13
replies
4.1k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
3.5 years ago • updated 3.3 years ago rohitsatyam102 ▴ 20
1
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1
reply
1.1k
views
cannot create GRanges object anymore
GenomicR GenomicRanges
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
vote
1
reply
920
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 2.3 years ago by ▴ 40 • written 7.9 years ago by ▴ 40
1
vote
1
reply
1.3k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.5 years ago by 65k • written 3.5 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 3.7 years ago by ▴ 80
0
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0
replies
852
views
annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
3.6 years ago Nala • 0
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Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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