Showing : GenomicRanges • reset
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
5 days ago info ▴ 10
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2
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
updated 5 weeks ago by 67k • written 5 weeks ago by ▴ 80
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222
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
11 weeks ago user_bioinfo • 0
2
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1
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319
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 6 months ago by 42k • written 6 months ago by ▴ 80
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342
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
7 months ago gshweta95 • 0
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
8 months ago mat149 ▴ 80
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1
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525
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
9 months ago mat149 ▴ 80
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2
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1000
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 18 months ago by • 0 • written 18 months ago by • 0
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4
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1.3k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 20 months ago by 16k • written 20 months ago by • 0
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1
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840
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Error printing a CompressedGRangesList
GenomicRanges
22 months ago • updated 20 months ago Lluís Revilla Sancho ▴ 760
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819
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
21 months ago Delta._.43 ▴ 20
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1.7k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 21 months ago by 67k • written 21 months ago by ★ 1.5k
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1
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884
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 22 months ago by 42k • written 22 months ago by • 0
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2
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1.5k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 24 months ago by ★ 1.6k • written 24 months ago by • 0
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2
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2.4k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.1 years ago Mog • 0
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712
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.3 years ago Simon Coetzee ▴ 50
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3
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2.3k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.4 years ago • updated 2.3 years ago Rodrigo • 0
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1.2k
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
3
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2
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1.7k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
2.5 years ago samantha.haque • 0
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2
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1.9k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
2.5 years ago vanbelj ▴ 30
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1.2k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.6 years ago Charles Plessy ▴ 180
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4.6k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.6 years ago by ▴ 20 • written 2.7 years ago by • 0
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6
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1.8k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
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920
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.7 years ago svlachavas ▴ 830
6
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2
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1.4k
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strand-aware GRanges shift
GenomicRanges
updated 2.8 years ago by ★ 1.6k • written 2.8 years ago by ▴ 10
9
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9
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3.9k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.8 years ago by 67k • written 2.8 years ago by ▴ 10
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5
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2.2k
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 40
4
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1
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911
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 180
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3
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6.3k
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Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.0 years ago by 67k • written 3.0 years ago by ▴ 10
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4
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3.6k
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.8 years ago by 16k • written 3.0 years ago by ▴ 20
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2
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1.3k
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Handling missing seqlenghts
GenomicRanges
3.0 years ago Charles Plessy ▴ 180
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2
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1.4k
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GenomicRanges::union fails on R devel
devel GenomicRanges
3.1 years ago Guillaume Devailly ▴ 60
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1.3k
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How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
3.1 years ago Pratik Mehta ▴ 10
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2
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1.5k
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How to subset GRangesList by seqnames
GenomicRanges
updated 3.2 years ago by 67k • written 3.2 years ago by ▴ 10
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2
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1.6k
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`GenomicRanges` cheat sheet
GenomicRanges
3.2 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
3.2 years ago Arslan • 0
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2
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1.1k
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GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
3.2 years ago Daniel Cameron ▴ 40
2
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4
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1.4k
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Unique GPos taking into account mcols
GenomicRanges unique GPos
3.3 years ago • updated 3.1 years ago maltethodberg ▴ 180
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1
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737
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How to overlap granges objects by gene name
GenomicRanges
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
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5
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3.5k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.4 years ago rtrivedi1 ▴ 10
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787
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.4 years ago Dario Strbenac ★ 1.5k
3
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2
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983
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Should I create a new class or using Common Classes
GenomicRanges
updated 3.5 years ago by 16k • written 3.5 years ago by ▴ 40
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0
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850
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.5 years ago alorsonmethyle • 0
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4
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1.7k
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.5 years ago Yixin • 0
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13
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5.0k
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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
3.9 years ago • updated 3.8 years ago rohitsatyam102 ▴ 20
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1.3k
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
1
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1
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1.1k
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Average coverage between multiple samples
GenomicRanges
updated 3.9 years ago by ★ 11k • written 3.9 years ago by ▴ 90
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10
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20k
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How do I merge a list of GRanges?
GenomicRanges
updated 2.8 years ago by ▴ 40 • written 8.4 years ago by ▴ 40
1
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1
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1.6k
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GenomicRanges equivalent to bedtools cluster
IRanges GenomicRanges
updated 4.0 years ago by 67k • written 4.0 years ago by • 0
50 results • Page 1 of 1
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Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Gordon Smyth 51k
`nec` computes one set of negative control parameters (mu, sigma, alpha) for each sample.
Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0
Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…
Answer: DESeq Input from Salmon + tximport/tximeta by Michael Love 42k
Given nf-core's pipeline here, you can use rounded counts from `gene_counts_length_scaled.tsv`.
Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k
You don't want to add a logFC on top like that, as it invalidates the p-value. Maybe I wasn't clear before. The LRT gives you all the gene…
Comment: Question about using LRT test for time course experiments with DESeq2 by Denise • 0
Hi James, Thank you very much for your very detailed explanation! I guess my question is simpler than that, I just want to union, across…
Votes
Answer: DESeq Input from Salmon + tximport/tximeta
Answer: featureCounts segmentation fault with large chromosomes
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
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