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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0
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194
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
10 weeks ago mat149 ▴ 70
2
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1
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258
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
12 weeks ago mat149 ▴ 70
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2
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768
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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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926
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 13 months ago by 16k • written 13 months ago by • 0
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1
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615
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Error printing a CompressedGRangesList
GenomicRanges
16 months ago • updated 14 months ago Lluís Revilla Sancho ▴ 730
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586
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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
3
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1
reply
706
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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 17 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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568
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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
reply
959
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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
23 months ago samantha.haque • 0
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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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968
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.0 years ago by ▴ 780 • written 2.1 years ago by • 0
1
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0
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778
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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 2.1 years ago by • 0
0
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6
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1.5k
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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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684
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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 2.2 years ago by ▴ 10
9
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9
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3.1k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.3 years ago by 65k • written 2.3 years ago by ▴ 10
3
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5
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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
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1
reply
741
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 2.5 years ago by 16k • written 2.5 years ago by ▴ 180
0
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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
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 2.6 years ago by 65k • written 2.6 years ago by ▴ 10
2
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2
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1.3k
views
`GenomicRanges` cheat sheet
GenomicRanges
2.6 years ago chirag.parsania • 0
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2
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1.0k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
2.6 years ago Arslan • 0
0
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2
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944
views
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
reply
620
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
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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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667
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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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781
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Should I create a new class or using Common Classes
GenomicRanges
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 40
0
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0
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713
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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
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 3.2 years ago rohitsatyam102 ▴ 20
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
892
views
Average coverage between multiple samples
GenomicRanges
updated 3.4 years ago by ★ 11k • written 3.4 years ago by ▴ 90
19
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10
replies
18k
views
How do I merge a list of GRanges?
GenomicRanges
updated 2.2 years ago by ▴ 40 • written 7.9 years ago by ▴ 40
1
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1
reply
1.2k
views
GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
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3
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1.9k
views
Merging Neighboring Genomic Segments
Granges GenomicRanges
3.5 years ago • updated 3.4 years ago rahnaman ▴ 10
2
votes
2
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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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829
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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
replies
1.2k
views
Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
3.6 years ago r.a.policastro • 0
50 results • Page 1 of 1
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Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
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