Showing : Genomicranges • reset
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Finding duplicated entries in GRangesList
GenomicRanges
updated 1 day 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 9 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
6 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
7 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
7 months ago 1324087964 • 0
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1
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1.3k
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 9 months ago by 43k • written 4.5 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 9 months ago by 43k • written 5.1 years ago by • 0
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409
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
12 months ago info ▴ 10
3
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3
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809
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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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529
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
15 months ago user_bioinfo • 0
2
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1
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619
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 18 months ago by 43k • written 18 months ago by ▴ 80
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783
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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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651
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
21 months ago mat149 ▴ 80
2
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1
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867
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Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
21 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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1.8k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
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1
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1.1k
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Error printing a CompressedGRangesList
GenomicRanges
2.9 years ago • updated 2.7 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
2.8 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 2.8 years ago by 68k • written 2.8 years ago by ★ 1.6k
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1
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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 2.9 years ago by 43k • written 2.9 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 3.0 years ago by ★ 1.6k • written 3.0 years ago by • 0
2
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2
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3.3k
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getSeq failing with DNAStringSet and GRanges
ORFik Bioconductor GenomicRanges Biostrings BSgenome
3.1 years ago Mog • 0
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0
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920
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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
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 3.4 years ago by 68k • written 3.4 years ago by • 0
3
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2
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2.2k
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toGRanges help!
GenomicRanges toGRanges Bioconductor
3.5 years ago samantha.haque • 0
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2
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2.4k
views
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 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
1
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0
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1.2k
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How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.6 years ago Charles Plessy ▴ 180
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2
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6.1k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.6 years ago by ▴ 20 • written 3.7 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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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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1.8k
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strand-aware GRanges shift
GenomicRanges
updated 3.8 years ago by ★ 1.6k • written 3.8 years ago by ▴ 10
9
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9
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5.1k
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 3.9 years ago by 16k • written 3.9 years ago by ▴ 40
4
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1
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1.2k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 4.0 years ago by 16k • written 4.0 years ago by ▴ 180
1
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3
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8.0k
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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
4.1 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
4.2 years ago Pratik Mehta ▴ 10
2
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2
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1.9k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 10
3
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2
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2.1k
views
`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
4.2 years ago Arslan • 0
0
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2
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1.4k
views
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
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
4.3 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
4.4 years ago rtrivedi1 ▴ 10
0
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0
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998
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
4.4 years ago Dario Strbenac ★ 1.6k
403 results • Page 1 of 9
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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