Showing : genomicranges • reset
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Job: Bioinformatician at the Lausanne University Hospital
GenomicRanges JobPosting
14 days ago story.benjamin ▴ 20
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244
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Finding duplicated entries in GRangesList
GenomicRanges
updated 18 days ago by ★ 4.0k • written 3 months ago by • 0
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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 12 weeks ago Kateřina • 0
4
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2
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1.3k
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GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
6 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
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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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1
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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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833
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
14 months ago • updated 11 months ago mat149 ▴ 80
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546
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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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630
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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
20 months ago gshweta95 • 0
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660
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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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1
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883
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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
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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 2.7 years ago by 16k • written 2.8 years ago by • 0
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1.2k
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Error printing a CompressedGRangesList
GenomicRanges
2.9 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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2.5k
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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
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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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928
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
3.4 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
3.4 years ago Rodrigo • 0
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1.7k
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
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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
3.6 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
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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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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
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2
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1.8k
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strand-aware GRanges shift
GenomicRanges
updated 3.8 years ago by ★ 1.6k • written 3.9 years ago by ▴ 10
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9
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5.1k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 10
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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
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1
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1.2k
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`promoters()` fails on `GPos` objects
GenomicRanges
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 180
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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
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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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1.8k
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Handling missing seqlenghts
GenomicRanges
4.1 years ago Charles Plessy ▴ 180
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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
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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
4.2 years ago Pratik Mehta ▴ 10
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2
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1.9k
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How to subset GRangesList by seqnames
GenomicRanges
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 10
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2
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2.1k
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`GenomicRanges` cheat sheet
GenomicRanges
4.2 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
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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
4.3 years ago Daniel Cameron ▴ 40
2
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4
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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
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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
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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
4.4 years ago rtrivedi1 ▴ 10
404 results • Page 1 of 9
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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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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