Showing : GenomicRanges • reset
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
7 weeks ago info ▴ 10
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3
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391
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
12 weeks ago • updated 1 day ago mat149 ▴ 80
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262
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
4 months ago user_bioinfo • 0
2
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1
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357
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 7 months ago by 43k • written 7 months ago by ▴ 80
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388
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
9 months ago gshweta95 • 0
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433
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
10 months ago mat149 ▴ 80
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1
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589
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
10 months ago mat149 ▴ 80
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1.0k
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 19 months ago by • 0 • written 20 months ago by • 0
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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 21 months ago by 16k • written 21 months ago by • 0
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1
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871
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Error printing a CompressedGRangesList
GenomicRanges
23 months ago • updated 22 months ago Lluís Revilla Sancho ▴ 760
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850
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
23 months ago Delta._.43 ▴ 20
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1.8k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 23 months ago by 67k • written 23 months ago by ★ 1.5k
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1
reply
916
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 24 months ago by 43k • written 24 months ago by • 0
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2
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1.6k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by • 0
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2
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2.6k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
2.2 years ago Mog • 0
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736
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
2.5 years ago Simon Coetzee ▴ 50
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3
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2.5k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
2.5 years ago Rodrigo • 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 2.5 years ago by 67k • written 2.5 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
2.6 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
2.7 years ago vanbelj ▴ 30
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1.3k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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983
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
2.7 years ago Charles Plessy ▴ 180
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4.8k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 2.7 years ago by ▴ 20 • written 2.8 years ago by • 0
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6
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1.9k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
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949
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
2.9 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 2.9 years ago by ★ 1.6k • written 2.9 years ago by ▴ 10
9
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9
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4.1k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 2.9 years ago by 67k • written 3.0 years ago by ▴ 10
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5
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2.3k
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 3.0 years ago by 16k • written 3.0 years ago by ▴ 40
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1
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936
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.1 years ago by 16k • written 3.1 years ago by ▴ 180
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3
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6.7k
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Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 10
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4
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3.8k
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 2.9 years ago by 16k • written 3.1 years ago by ▴ 20
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2
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1.4k
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Handling missing seqlenghts
GenomicRanges
3.2 years ago • updated 3.1 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
3.2 years ago Guillaume Devailly ▴ 60
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2
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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
3.3 years ago Pratik Mehta ▴ 10
2
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2
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1.5k
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How to subset GRangesList by seqnames
GenomicRanges
updated 3.3 years ago by 67k • written 3.3 years ago by ▴ 10
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2
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1.7k
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`GenomicRanges` cheat sheet
GenomicRanges
3.3 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
3.3 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
3.4 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
3.4 years ago • updated 3.2 years ago maltethodberg ▴ 180
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764
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How to overlap granges objects by gene name
GenomicRanges
updated 3.4 years ago by 67k • written 3.4 years ago by • 0
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5
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3.7k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
3.5 years ago rtrivedi1 ▴ 10
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813
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
3.5 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 3.6 years ago by 16k • written 3.6 years ago by ▴ 40
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0
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877
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
3.6 years ago alorsonmethyle • 0
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4
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1.8k
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IRanges::findOverlapPairs cannot take inputs if they are too large
IRanges GenomicRanges
3.6 years ago Yixin • 0
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13
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5.2k
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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
4.1 years ago • updated 3.9 years ago rohitsatyam102 ▴ 20
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1
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1.3k
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cannot create GRanges object anymore
GenomicR GenomicRanges
updated 3.9 years ago by 67k • written 3.9 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 4.0 years ago by ★ 11k • written 4.0 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 2.9 years ago by ▴ 40 • written 8.5 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 4.1 years ago by 67k • written 4.1 years ago by • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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