Showing : genomicranges • reset
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 1 day ago by 43k • written 3.8 years ago by • 0
0
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1
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1.5k
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 1 day ago by 43k • written 4.3 years ago by • 0
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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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462
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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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296
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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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394
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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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426
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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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461
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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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630
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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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907
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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 2.0 years ago by 67k • written 2.0 years ago by ★ 1.5k
3
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1
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946
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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 2.2 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
2.3 years ago Mog • 0
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0
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756
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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
0
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1
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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
1
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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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0
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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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4.9k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.8 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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978
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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 3.1 years ago by ▴ 40
4
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1
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961
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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
views
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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1.4k
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GenomicRanges::union fails on R devel
devel GenomicRanges
3.3 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
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`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
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
views
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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802
views
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
0
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0
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833
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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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1.0k
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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
views
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
views
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
reply
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
views
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: displaying the differential expression with deseq2 over 4X2 samples with the in by Martijn • 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA? by jodan • 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Votes
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?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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