Showing : summarizeoverlaps • reset
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
3.4 years ago dequattro.concetta ▴ 10
4
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3
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900
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Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 3.6 years ago by 64k • written 3.6 years ago by ▴ 10
0
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9
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1.2k
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summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
1
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9
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1.2k
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Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 4.8 years ago by 64k • written 4.8 years ago by ▴ 10
0
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1
reply
950
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counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 5.6 years ago by ★ 6.8k • written 5.7 years ago by • 0
2
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2
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965
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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 5.6 years ago by ★ 6.8k • written 5.6 years ago by 7.8k
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0
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858
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
5.7 years ago A ▴ 40
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0
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1.0k
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large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
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6
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1.3k
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deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
5.7 years ago cosmin • 0
0
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2
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867
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Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps R
updated 5.8 years ago by ★ 6.8k • written 5.8 years ago by • 0
1
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1
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1.6k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 5.8 years ago by 64k • written 5.8 years ago by • 0
1
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1
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1.8k
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Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 6.1 years ago by ▴ 160 • written 6.1 years ago by ▴ 10
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2
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1.0k
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Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 10
1
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0
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1.1k
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readGAlignmentPairs
6.7 years ago teresati ▴ 10
1
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1
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1.2k
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summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 6.8 years ago by 16k • written 6.8 years ago by ▴ 10
3
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3
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1.6k
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Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 6.8 years ago by 16k • written 6.8 years ago by ▴ 10
2
votes
2
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784
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question about summrizeOverlaps
summarizeoverlaps
updated 6.8 years ago by 25k • written 6.8 years ago by ★ 1.3k
0
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1
reply
1.0k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 6.8 years ago by 64k • written 6.8 years ago by ▴ 40
2
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6
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1.3k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 7.0 years ago by 41k • written 7.0 years ago by • 0
2
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3
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1.9k
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SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 7.1 years ago by ★ 1.7k • written 7.1 years ago by • 0
1
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1
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2.1k
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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
7.2 years ago chriad ▴ 10
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5
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1.6k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
7.3 years ago philipp.wahle • 0
4
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3
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2.8k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
7.4 years ago ErickF ▴ 40
2
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2
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1.5k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
7.5 years ago • updated 7.4 years ago Jon Manning ▴ 90
2
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9
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1.5k
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SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 7.7 years ago by ★ 6.8k • written 7.7 years ago by ▴ 10
0
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3
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1.6k
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summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
7.7 years ago vedran.franke • 0
2
votes
7
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1.8k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
7.8 years ago • updated 7.7 years ago tmartinez • 0
0
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1
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1.0k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
7.8 years ago diogo.camacho.2008 • 0
0
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2
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1.5k
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Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 7.8 years ago by 41k • written 7.8 years ago by • 0
0
votes
1
reply
1.4k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 7.8 years ago by ★ 6.8k • written 7.8 years ago by • 0
4
votes
11
replies
2.1k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 7.8 years ago by ★ 6.8k • written 7.8 years ago by ▴ 10
1
vote
4
replies
1.4k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 7.8 years ago by 16k • written 7.9 years ago by ▴ 570
2
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4
replies
2.3k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
7.9 years ago bioprog • 0
1
vote
2
replies
953
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 8.0 years ago by 13k • written 8.0 years ago by • 0
2
votes
5
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2.7k
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GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.0 years ago by ★ 6.8k • written 8.0 years ago by ▴ 30
0
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3
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1.3k
views
Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
8.2 years ago Pau Marc Muñoz Torres ▴ 20
8
votes
9
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5.7k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.4 years ago by • 0 • written 8.4 years ago by ★ 1.5k
0
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20
replies
5.6k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 8.4 years ago by ▴ 90 • written 8.4 years ago by ▴ 10
11
votes
8
replies
4.2k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 10
0
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1
reply
1.5k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 8.7 years ago by ★ 6.8k • written 8.7 years ago by 6.7k
6
votes
14
replies
5.5k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 8.9 years ago by 48k • written 8.9 years ago by • 0
0
votes
3
replies
2.2k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 9.0 years ago by ★ 8.2k • written 9.0 years ago by ▴ 20
42 results • Page 1 of 1
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Answer: EdgeR: Exact test and glmQLFTest produce very different results by James W. MacDonald 64k
You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.
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The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…
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I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…
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It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor by arina • 0
Hi Omer, Unfortunately I don't have an answer to your issue, but I am facing a very similar problem after integrating datasets that were …
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