Showing : GenomicRanges • reset
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Job: Bioinformatician at the Lausanne University Hospital
GenomicRanges JobPosting
written 22 days ago by ▴ 20
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263
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Finding duplicated entries in GRangesList
GenomicRanges
updated 26 days ago by ★ 4.0k • written 3 months ago by • 0
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4
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How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges tidySummarizedExperiment tidyomics
7 months ago • updated 3 months ago Kateřina • 0
4
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2
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1.4k
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GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
7 months ago pineiroalejandro ▴ 10
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
7 months ago jamiecatalano2 • 0
1
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4
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1.1k
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fast apply on RleList
GenomicRanges RleList
8 months ago story.benjamin ▴ 20
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1.1k
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Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges CNEr
8 months ago 1324087964 • 0
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1.3k
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 10 months ago by 43k • written 4.6 years ago by • 0
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2.0k
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 10 months ago by 43k • written 5.2 years ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
13 months ago info ▴ 10
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3
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840
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
14 months ago • updated 12 months ago mat149 ▴ 80
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562
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
16 months ago user_bioinfo • 0
2
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1
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636
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 19 months ago by 43k • written 19 months ago by ▴ 80
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
21 months ago gshweta95 • 0
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667
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
22 months ago mat149 ▴ 80
2
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896
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
22 months ago mat149 ▴ 80
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2
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1.4k
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
3
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4
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1.9k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.8 years ago by 16k • written 2.8 years ago by • 0
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1
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1.2k
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Error printing a CompressedGRangesList
GenomicRanges
3.0 years ago • updated 2.8 years ago Lluís Revilla Sancho ▴ 760
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1.1k
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.9 years ago Delta._.43 ▴ 20
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4
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2.6k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.9 years ago by 68k • written 2.9 years ago by ★ 1.6k
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1.2k
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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2
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2.1k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by • 0
2
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2
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3.4k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.2 years ago Mog • 0
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938
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
3.5 years ago Simon Coetzee ▴ 50
2
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3
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3.2k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
3.5 years ago Rodrigo • 0
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1
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1.7k
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
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2
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2.2k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
3.6 years ago samantha.haque • 0
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2
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2.4k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.7 years ago vanbelj ▴ 30
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1
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1.7k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
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1.3k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.7 years ago Charles Plessy ▴ 180
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6.1k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.7 years ago by ▴ 20 • written 3.8 years ago by • 0
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6
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2.5k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
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1.2k
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Annotating copy number alterations per sample using CNVRanger R package and return of duplicated gene symbols
CopyNumberVariation CNVRanger GenomicRanges
3.8 years ago svlachavas ▴ 840
6
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2
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1.9k
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strand-aware GRanges shift
GenomicRanges
updated 3.9 years ago by ★ 1.6k • written 3.9 years ago by ▴ 10
9
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9
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5.2k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 10
3
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5
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2.8k
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 40
4
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1
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1.2k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 180
1
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3
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8.1k
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Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 10
2
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4
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4.7k
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.9 years ago by 16k • written 4.1 years ago by ▴ 20
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2
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1.8k
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Handling missing seqlenghts
GenomicRanges
4.1 years ago Charles Plessy ▴ 180
4
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2
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1.7k
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GenomicRanges::union fails on R devel
devel GenomicRanges
4.2 years ago Guillaume Devailly ▴ 60
5
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2
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1.7k
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How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.3 years ago Pratik Mehta ▴ 10
2
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2
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1.9k
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How to subset GRangesList by seqnames
GenomicRanges
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 10
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2
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2.1k
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`GenomicRanges` cheat sheet
GenomicRanges
4.3 years ago chirag.parsania ▴ 10
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2
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1.6k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
4.3 years ago Arslan • 0
0
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2
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1.5k
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GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
4.4 years ago • updated 4.3 years ago Daniel Cameron ▴ 40
2
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4
replies
1.9k
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Unique GPos taking into account mcols
GenomicRanges unique GPos
4.4 years ago • updated 4.2 years ago maltethodberg ▴ 180
0
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1
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1.0k
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How to overlap granges objects by gene name
GenomicRanges
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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5
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4.5k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.5 years ago rtrivedi1 ▴ 10
404 results • Page 1 of 9
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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