Showing : GenomicRanges • reset
2
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Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures Guitar txdbmaker GenomicRanges
written 23 days ago by ▴ 10
0
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1
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309
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Job: Bioinformatician at the Lausanne University Hospital
GenomicRanges JobPosting
written 8 weeks ago by ▴ 20
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1
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343
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Finding duplicated entries in GRangesList
GenomicRanges
updated 8 weeks ago by ★ 4.0k • written 5 months ago by • 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
8 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
9 months ago jamiecatalano2 • 0
1
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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
9 months ago • updated 4 months ago Kateřina • 0
1
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4
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1.2k
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fast apply on RleList
GenomicRanges RleList
9 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
9 months ago 1324087964 • 0
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462
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
14 months ago info ▴ 10
3
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3
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880
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
16 months ago • updated 13 months ago mat149 ▴ 80
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604
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
17 months ago user_bioinfo • 0
2
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1
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671
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 20 months ago by 43k • written 20 months ago by ▴ 80
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822
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
22 months ago gshweta95 • 0
0
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0
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693
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
23 months ago mat149 ▴ 80
2
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1
reply
947
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
23 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 2.7 years ago by • 0 • written 2.7 years ago by • 0
3
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4
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2.0k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.9 years ago by 16k • written 2.9 years ago by • 0
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0
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1.2k
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Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
3.0 years ago Delta._.43 ▴ 20
4
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4
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2.6k
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Flank GenomicRanges on Both Sides
GenomicRanges
updated 3.0 years ago by 68k • written 3.0 years ago by ★ 1.6k
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1
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1.2k
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Error printing a CompressedGRangesList
GenomicRanges
3.1 years ago • updated 2.9 years ago Lluís Revilla Sancho ▴ 760
3
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1
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1.3k
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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2
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2.2k
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GenomicRanges method to make the total width of ranges a certain value?
GenomicRanges
updated 3.2 years ago by ★ 1.6k • written 3.2 years ago by • 0
2
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2
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3.5k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.3 years ago Mog • 0
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0
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957
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nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
3.6 years ago Simon Coetzee ▴ 50
2
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3
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3.3k
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Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
3.6 years ago Rodrigo • 0
0
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1
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1.8k
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Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
3
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2
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2.3k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
3.7 years ago samantha.haque • 0
1
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2
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2.5k
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Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.8 years ago vanbelj ▴ 30
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1
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1.8k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
1
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0
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1.3k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.8 years ago Charles Plessy ▴ 180
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6
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2.6k
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Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
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2
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6.3k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.8 years ago by ▴ 20 • written 3.9 years ago by • 0
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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
3.9 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 4.0 years ago by ★ 1.6k • written 4.0 years ago by ▴ 10
9
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9
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5.3k
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Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 10
3
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5
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3.0k
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Splitting a TxDB or GRanges by Chromosome
GenomicRanges split chromosome TxDb
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 40
4
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1
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1.2k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 4.2 years ago by 16k • written 4.2 years ago by ▴ 180
1
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3
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8.3k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 10
2
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4
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4.9k
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 4.0 years ago by 16k • written 4.2 years ago by ▴ 20
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2
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1.9k
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Handling missing seqlenghts
GenomicRanges
4.2 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
4.3 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
4.4 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 4.4 years ago by 68k • written 4.4 years ago by ▴ 10
3
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2
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2.2k
views
`GenomicRanges` cheat sheet
GenomicRanges
4.4 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
4.4 years ago Arslan • 0
0
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2
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1.5k
views
GRanges::distanceToNearest does not return distance to nearest
GenomicRanges Genomic
4.5 years ago • updated 4.4 years ago Daniel Cameron ▴ 40
2
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4
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2.0k
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Unique GPos taking into account mcols
GenomicRanges unique GPos
4.5 years ago • updated 4.3 years ago maltethodberg ▴ 180
0
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1
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1.1k
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How to overlap granges objects by gene name
GenomicRanges
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
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5
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4.6k
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Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.6 years ago rtrivedi1 ▴ 10
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0
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1.0k
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
4.6 years ago Dario Strbenac ★ 1.6k
405 results • Page 1 of 9
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Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Julia Broadbent • 0
Hi Emily, Just sharing a resource for handling contaminants - we use the methods described in [Frankenfield et al. (2022)](https://pubs.acs…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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