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Memory issues in summarizeOverlaps funtion
summarizeoverlaps memory written 15 days ago by Diana • 10 • updated 15 days ago by James W. MacDonald ♦ 49k
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counting reads with muliple hits with SummarizeOverlaps
R ngs summarizeoverlaps seq written 10 months ago by Lolla • 0 • updated 10 months ago by Valerie Obenchain • 6.7k
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How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
genomicalignments summarizeoverlaps written 10 months ago by Ryan C. Thompson ♦ 7.2k • updated 10 months ago by Valerie Obenchain • 6.7k
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Metadata sheet for DEXSeq analysis
dexseq granges summarizeoverlaps isoforms differential isoform usage written 10 months ago by A • 40
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large memory footprint with summarizeOverlaps method for BamViews
rsamtools genomicalignments summarizeoverlaps bamviews written 11 months ago by alex.gos90 • 10 • updated 11 months ago by Martin Morgan ♦♦ 23k
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deconvole counts per feature from summerizedOverlaps with GRangesLists
grangeslist summarizeoverlaps summarizedexperiment rangedsummarizedexperiment written 11 months ago by cosmin • 0
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Minimum overlap for reads to be counted in summarizeoverlaps
R summarizeoverlaps written 12 months ago by Lolla • 0 • updated 12 months ago by Valerie Obenchain • 6.7k
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How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix written 12 months ago by johnsonn573 • 0 • updated 12 months ago by James W. MacDonald ♦ 49k
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Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts written 15 months ago by Walter F. Baumann • 10 • updated 15 months ago by thokall • 120
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Problems with summarizeOverlaps
rnaseq bioconductor summarizeoverlaps written 21 months ago by Walter F. Baumann • 10 • updated 21 months ago by Martin Morgan ♦♦ 23k
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readgalignmentpairs written 23 months ago by teresati • 10
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summarizeOverlaps counting exons and 5UTR reads
rnaseq summarizeoverlaps written 24 months ago by Walter F. Baumann • 10 • updated 24 months ago by Hervé Pagès ♦♦ 13k
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Comparing two RNAseq experiments using summarizeOverlaps
rnaseq R bioconductor summarizeoverlaps rna-seq written 24 months ago by Walter F. Baumann • 10 • updated 24 months ago by Hervé Pagès ♦♦ 13k
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question about summrizeOverlaps
summarizeoverlaps written 2.0 years ago by Ou, Jianhong • 1.1k • updated 2.0 years ago by Martin Morgan ♦♦ 23k
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GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
genomicalignments summarizeoverlaps written 2.0 years ago by JunLVI • 40 • updated 2.0 years ago by James W. MacDonald ♦ 49k
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DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
genomicfeatures genomicalignments bioclite bioconductor summarizeoverlaps written 2.2 years ago by BioinfStudent • 0 • updated 2.2 years ago by Michael Love ♦ 22k
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SystemPipeR: alignments with ambiguous pairing were dumped.
rnaseq R systempiper summarizeoverlaps tophat written 2.3 years ago by abass.conteh • 0 • updated 2.3 years ago by Thomas Girke • 1.7k
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Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
biocparallel software error summarizeoverlaps written 2.5 years ago by chriad • 10
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summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
genomicalignments summarizeoverlaps written 2.5 years ago by philipp.wahle • 0
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Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
rnaseq summarizeoverlaps bplapply read counting rangedsummarizedexperiment written 2.6 years ago by ErickF • 20
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Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps written 2.7 years ago by Jon Manning • 90
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SummarizeOverlaps without reference genome ?
summarizeoverlaps written 2.9 years ago by jean.keller • 10 • updated 2.9 years ago by Valerie Obenchain • 6.7k
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summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps written 3.0 years ago by vedran.franke • 0
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Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools written 3.0 years ago by tmartinez • 0
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No reads with summarizeOverlaps
rnaseq summarizeoverlaps written 3.0 years ago by diogo.camacho.2008 • 0
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