Showing : summarizeOverlaps • reset
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
3.8 years ago dequattro.concetta ▴ 10
4
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3
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1.0k
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Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 10
0
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9
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1.4k
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summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
1
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9
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1.3k
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Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 5.2 years ago by 65k • written 5.2 years ago by ▴ 10
2
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2
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1.1k
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How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by ★ 7.9k
0
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1
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1.0k
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counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 6.0 years ago by ★ 6.8k • written 6.1 years ago by • 0
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0
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961
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
6.1 years ago A ▴ 40
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0
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1.2k
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large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 10
1
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6
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1.5k
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deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.1 years ago cosmin • 0
0
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2
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994
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Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps R
updated 6.2 years ago by ★ 6.8k • written 6.2 years ago by • 0
1
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1
reply
1.9k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 6.2 years ago by 65k • written 6.2 years ago by • 0
1
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1
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2.0k
views
Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 6.5 years ago by ▴ 160 • written 6.5 years ago by ▴ 10
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2
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1.1k
views
Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 10
1
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0
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1.2k
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readGAlignmentPairs
7.1 years ago teresati ▴ 10
1
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1
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1.3k
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
3
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3
replies
1.8k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
2
votes
2
replies
882
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question about summrizeOverlaps
summarizeoverlaps
updated 7.2 years ago by 25k • written 7.2 years ago by ★ 1.3k
0
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1
reply
1.1k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 40
2
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6
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1.4k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
2
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3
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2.1k
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SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 7.5 years ago by ★ 1.7k • written 7.5 years ago by • 0
1
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1
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2.2k
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Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
software error summarizeoverlaps biocParallel
7.6 years ago chriad ▴ 10
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5
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1.7k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
7.7 years ago philipp.wahle • 0
4
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3
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2.9k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
7.8 years ago ErickF ▴ 40
2
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2
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1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 23 days ago by • 0 • written 7.9 years ago by ▴ 90
2
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9
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1.6k
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SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 10
0
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3
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1.7k
views
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
8.1 years ago vedran.franke • 0
2
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7
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2.0k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
8.1 years ago tmartinez • 0
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1
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1.1k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
8.2 years ago diogo.camacho.2008 • 0
0
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2
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1.6k
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Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
0
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1
reply
1.5k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by • 0
4
votes
11
replies
2.3k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ▴ 10
1
vote
4
replies
1.5k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 570
2
votes
4
replies
2.5k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.3 years ago bioprog • 0
1
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2
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1.1k
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 8.4 years ago by ★ 13k • written 8.4 years ago by • 0
2
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5
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2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 30
0
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3
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1.4k
views
Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
8.6 years ago • updated 8.5 years ago Pau Marc Muñoz Torres ▴ 20
0
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20
replies
6.1k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 10
8
votes
9
replies
6.0k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.8 years ago by • 0 • written 8.8 years ago by ★ 1.5k
11
votes
8
replies
4.4k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
0
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1
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1.6k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by 6.7k
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
0
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3
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2.4k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 9.4 years ago by ★ 8.2k • written 9.4 years ago by ▴ 20
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Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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