Showing : genomicranges • reset
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Finding duplicated entries in GRangesList
GenomicRanges
9 weeks ago Marco • 0
1
vote
4
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2.0k
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How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges tidySummarizedExperiment tidyomics
6 months ago • updated 5 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
5 months ago pineiroalejandro ▴ 10
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0
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418
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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
vote
4
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1.1k
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fast apply on RleList
GenomicRanges RleList
6 months ago story.benjamin ▴ 20
2
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1
reply
1.0k
views
Having Trouble Using CNE12() and CNE21() in CNEr
GenomicRanges CNEr
6 months ago 1324087964 • 0
0
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1
reply
1.2k
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Using genomicRanges / plyranges to calculate score of peaks within intervals
plyranges GenomicRanges
updated 8 months ago by 43k • written 4.5 years ago by • 0
1
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1
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1.9k
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Reducing and aggregating GRanges with gaps using plyranges
GenomicRanges plyranges
updated 8 months ago by 43k • written 5.0 years ago by • 0
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0
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392
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
12 months ago info ▴ 10
3
votes
3
replies
783
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
13 months ago • updated 10 months ago mat149 ▴ 80
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0
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498
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hichip fragments extraction chip seq
ChIPSeqData interact GenomicRanges HiC
14 months ago user_bioinfo • 0
2
votes
1
reply
594
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 17 months ago by 43k • written 17 months ago by ▴ 80
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0
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657
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Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
19 months ago gshweta95 • 0
0
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0
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640
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ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
20 months ago mat149 ▴ 80
2
votes
1
reply
840
views
Need Help w/ Subset on GRangesList
GenomicRange GenomicRanges
21 months ago • updated 20 months ago mat149 ▴ 80
0
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2
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1.3k
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
3
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4
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1.8k
views
Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.6 years ago by 16k • written 2.6 years ago by • 0
0
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1
reply
1.1k
views
Error printing a CompressedGRangesList
GenomicRanges
2.8 years ago • updated 2.7 years ago Lluís Revilla Sancho ▴ 760
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0
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1.0k
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.8 years ago Delta._.43 ▴ 20
4
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4
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2.5k
views
Flank GenomicRanges on Both Sides
GenomicRanges
updated 2.8 years ago by 68k • written 2.8 years ago by ★ 1.6k
3
votes
1
reply
1.1k
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Find ranges that are shared by 80% or more of 10 GRanges objects
Granges GenomicRanges
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
2
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2.0k
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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
votes
2
replies
3.3k
views
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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897
views
nearest and nearestKNeighbors with k=1 produce different results
GenomicRanges
3.3 years ago Simon Coetzee ▴ 50
2
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3
replies
3.1k
views
Combine GRanges(List) to a single GRanges with unified breakpoints
GenomicRanges plyranges
3.3 years ago Rodrigo • 0
0
votes
1
reply
1.6k
views
Can´t install GenomicRanges and rtracklayer
rtracklayer GenomicRanges Installation
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
3
votes
2
replies
2.2k
views
toGRanges help!
GenomicRanges toGRanges Bioconductor
3.5 years ago samantha.haque • 0
1
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2
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2.3k
views
Extracting Score/Coverage From GRange Object
IRanges rtracklayer GenomicRanges
3.5 years ago vanbelj ▴ 30
0
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1
reply
1.7k
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finding overlap using GenomicRanges with two data sets specifying minoverlap Function
Biostrings GenomicRanges
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
1
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0
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1.2k
views
How about a getSeq() method for GRanges ?
GenomicRanges BSGenome
3.5 years ago Charles Plessy ▴ 180
0
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2
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5.9k
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Gene body coverage plot
plot gene GenomicRanges Coverage R
updated 3.6 years ago by ▴ 20 • written 3.6 years ago by • 0
0
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6
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2.4k
views
Error: duplicate row.names
GenomicRanges methylKit S4Vectors
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
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
3.7 years ago svlachavas ▴ 840
6
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2
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1.8k
views
strand-aware GRanges shift
GenomicRanges
updated 3.7 years ago by ★ 1.6k • written 3.7 years ago by ▴ 10
9
votes
9
replies
5.0k
views
Subset GRanges by intersection
findOverlaps GPos GenomicRanges subsetByOverlaps
updated 3.8 years ago by 68k • written 3.8 years ago by ▴ 10
3
votes
5
replies
2.8k
views
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
reply
1.1k
views
`promoters()` fails on `GPos` objects
GenomicRanges
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 180
1
vote
3
replies
8.0k
views
Understanding findoverlaps function in GenomicRanges
GenomicRanges genomicra
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 10
2
votes
4
replies
4.6k
views
How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 3.8 years ago by 16k • written 4.0 years ago by ▴ 20
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2
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1.8k
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Handling missing seqlenghts
GenomicRanges
4.0 years ago Charles Plessy ▴ 180
4
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2
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1.6k
views
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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1.6k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.1 years ago Pratik Mehta ▴ 10
2
votes
2
replies
1.8k
views
How to subset GRangesList by seqnames
GenomicRanges
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 10
3
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2
replies
2.1k
views
`GenomicRanges` cheat sheet
GenomicRanges
4.1 years ago chirag.parsania ▴ 10
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2
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1.5k
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Failed to get promoters using promoters() in R 4.0.3.
promoter GenomicRanges rtracklayer GRanges
4.1 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
4.2 years ago Daniel Cameron ▴ 40
2
votes
4
replies
1.8k
views
Unique GPos taking into account mcols
GenomicRanges unique GPos
4.3 years ago • updated 4.1 years ago maltethodberg ▴ 180
0
votes
1
reply
1.0k
views
How to overlap granges objects by gene name
GenomicRanges
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
5
replies
4.4k
views
Grange object subsetting using seqnames
Seqnames makeGRangesFromDataFrame GRanges Subsetting GenomicRanges
4.3 years ago rtrivedi1 ▴ 10
0
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0
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982
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Arithmetic Operations Between GRanges' Scores
GenomicRanges
4.4 years ago Dario Strbenac ★ 1.6k
403 results • Page 1 of 9
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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