Showing : Genomicranges • reset
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 4 hours ago by 41k • written 5 hours ago by ▴ 70
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124
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
6 weeks ago gshweta95 • 0
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0
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200
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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
267
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
3 months ago mat149 ▴ 70
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2
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773
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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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940
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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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1
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625
views
Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
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597
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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
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 15 months ago by 65k • written 15 months ago by ★ 1.5k
3
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1
reply
715
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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
views
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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576
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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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966
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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
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
24 months ago samantha.haque • 0
1
vote
2
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1.5k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.0 years ago vanbelj ▴ 30
0
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1
reply
976
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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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781
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.1 years ago Charles Plessy ▴ 180
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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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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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0
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695
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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 2.3 years ago by ★ 1.6k • written 2.3 years ago by ▴ 10
9
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9
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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
750
views
`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
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
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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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1.1k
views
Handling missing seqlenghts
GenomicRanges
2.5 years ago Charles Plessy ▴ 180
4
votes
2
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1.2k
views
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
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
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2
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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
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1.3k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.7 years ago chirag.parsania • 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
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2
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951
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
2.7 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 2.6 years ago maltethodberg ▴ 180
0
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1
reply
625
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
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5
replies
2.6k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
2.9 years ago • updated 2.8 years ago rtrivedi1 ▴ 10
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0
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670
views
Arithmetic Operations Between GRanges' Scores
GenomicRanges
2.9 years ago Dario Strbenac ★ 1.5k
3
votes
2
replies
790
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
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0
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717
views
Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.0 years ago alorsonmethyle • 0
1
vote
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
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
1.1k
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
900
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
1.2k
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 3.6 years ago by ▴ 80
0
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0
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837
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annotatr package: GRanges object contains out-of-bound ranges
annotatr GenomicRanges
3.5 years ago Nala • 0
50 results • Page 1 of 1
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by gene_bioconductor ▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
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Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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