Showing : Genomicranges • reset
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 3 days ago by 43k • written 3.8 years ago by • 0
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1
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1.6k
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 3 days ago by 43k • written 4.3 years ago by • 0
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170
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
3 months ago info ▴ 10
3
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3
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463
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
4 months ago • updated 6 weeks ago mat149 ▴ 80
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298
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
5 months ago user_bioinfo • 0
2
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1
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398
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 9 months ago by 43k • written 9 months ago by ▴ 80
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431
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
10 months ago gshweta95 • 0
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464
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
11 months ago mat149 ▴ 80
2
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1
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632
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
12 months ago mat149 ▴ 80
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2
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1.1k
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 21 months ago by • 0 • written 21 months ago by • 0
3
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4
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1.4k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 23 months ago by 16k • written 23 months ago by • 0
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1
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910
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Error printing a CompressedGRangesList
GenomicRanges
2.1 years ago • updated 23 months ago Lluís Revilla Sancho ▴ 760
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879
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.0 years ago Delta._.43 ▴ 20
4
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4
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1.9k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.1 years ago by 67k • written 2.1 years ago by ★ 1.5k
3
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1
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950
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 2.2 years ago by ★ 1.6k • written 2.3 years ago by • 0
2
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2
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2.7k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.4 years ago • updated 2.3 years ago Mog • 0
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758
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.6 years ago Simon Coetzee ▴ 50
2
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3
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2.6k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.6 years ago Rodrigo • 0
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1.3k
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
3
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2
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1.8k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
2.7 years ago samantha.haque • 0
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2
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2.0k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.8 years ago vanbelj ▴ 30
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1
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1.4k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
1
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1.0k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.8 years ago Charles Plessy ▴ 180
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2
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5.0k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.9 years ago by ▴ 20 • written 2.9 years ago by • 0
0
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6
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1.9k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
0
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0
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982
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
3.0 years ago svlachavas ▴ 840
6
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2
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1.5k
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strand-aware GRanges shift
GenomicRanges
updated 3.0 years ago by ★ 1.6k • written 3.0 years ago by ▴ 10
9
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9
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4.2k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 10
3
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5
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2.4k
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.1 years ago by 16k • written 3.2 years ago by ▴ 40
4
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1
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965
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.2 years ago by 16k • written 3.2 years ago by ▴ 180
1
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3
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6.9k
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Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.3 years ago by 67k • written 3.3 years ago by ▴ 10
2
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4
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4.0k
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.1 years ago by 16k • written 3.3 years ago by ▴ 20
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2
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1.5k
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Handling missing seqlenghts
GenomicRanges
3.3 years ago Charles Plessy ▴ 180
4
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2
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1.5k
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GenomicRanges::union fails on R devel
devel GenomicRanges
3.4 years ago Guillaume Devailly ▴ 60
5
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2
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1.4k
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How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.4 years ago Pratik Mehta ▴ 10
2
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2
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1.6k
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How to subset GRangesList by seqnames
GenomicRanges
updated 3.4 years ago by 67k • written 3.4 years ago by ▴ 10
3
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2
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1.8k
views
`GenomicRanges` cheat sheet
GenomicRanges
3.4 years ago chirag.parsania ▴ 10
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2
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1.3k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
3.4 years ago Arslan • 0
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2
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1.2k
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GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
3.5 years ago Daniel Cameron ▴ 40
2
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4
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1.5k
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Unique GPos taking into account mcols
GenomicRanges unique GPos
3.5 years ago • updated 3.4 years ago maltethodberg ▴ 180
0
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1
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804
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How to overlap granges objects by gene name
GenomicRanges
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
0
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5
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3.8k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.6 years ago rtrivedi1 ▴ 10
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0
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837
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.6 years ago Dario Strbenac ★ 1.5k
3
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2
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1.1k
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Should I create a new class or using Common Classes
GenomicRanges
updated 3.7 years ago by 16k • written 3.7 years ago by ▴ 40
1
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4
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1.9k
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.8 years ago • updated 3.7 years ago Yixin • 0
11
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13
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5.3k
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How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic AnnotationHub GenomicRanges org.Hs.eg.db
4.2 years ago • updated 4.0 years ago rohitsatyam102 ▴ 20
1
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1
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1.4k
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
1
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1
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1.2k
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Average coverage between multiple samples
GenomicRanges
updated 4.1 years ago by ★ 11k • written 4.1 years ago by ▴ 90
20
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10
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20k
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How do I merge a list of GRanges?
GenomicRanges
updated 3.0 years ago by ▴ 40 • written 8.6 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: GenomeInfoDbData cannot install in R and warning had non-zero exit status by Renuka • 0
how you did it pls explain
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by James W. MacDonald 67k
If I understand correctly, you want to assess differential transcript abundances. If so, there are a couple of ways you can do that. One wa…
Answer: Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes by a.alkema • 0
Oh, that's silly - thanks, will do!
Answer: Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes by James W. MacDonald 67k
This support site is meant to provide support for Bioconductor packages, but `Meffil` is not part of Bioconductor. You could presumably con…
Comment: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
> It looks like the ssgseaParam function might not be passing the > correct parameters to GSVA::gsva() Apparently because of the extra com…
Votes
Comment: Unused arguments error without used arguments in GSVA?
Answer: Reducing and aggregating GRanges with gaps using plyranges
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
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