Showing : summarizeOverlaps • reset
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
5.2 years ago dequattro.concetta ▴ 10
4
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3
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1.5k
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Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 10
0
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9
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2.0k
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summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 6.3 years ago by 25k • written 6.3 years ago by • 0
1
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9
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2.0k
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Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
0
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1
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1.4k
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counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by • 0
2
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2
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1.5k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 7.4 years ago by ★ 6.8k • written 7.4 years ago by ★ 7.9k
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0
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1.3k
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
7.5 years ago A ▴ 60
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0
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1.5k
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large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
1
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6
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2.1k
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deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
7.5 years ago cosmin • 0
0
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2
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1.4k
views
Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps R
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by • 0
1
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1
reply
2.4k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
1
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1
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2.7k
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Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 7.9 years ago by ▴ 160 • written 7.9 years ago by ▴ 10
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2
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1.4k
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Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 10
1
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0
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1.4k
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readGAlignmentPairs
8.4 years ago teresati ▴ 10
1
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1
reply
1.6k
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 8.5 years ago by 16k • written 8.5 years ago by ▴ 10
3
votes
3
replies
2.2k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 8.5 years ago by 16k • written 8.6 years ago by ▴ 10
2
votes
2
replies
1.1k
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question about summrizeOverlaps
summarizeoverlaps
updated 8.6 years ago by 25k • written 8.6 years ago by ★ 1.3k
0
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1
reply
1.5k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 40
2
votes
6
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1.9k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
2
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3
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2.6k
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SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 8.8 years ago by ★ 1.7k • written 8.8 years ago by • 0
1
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1
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2.5k
views
Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
software error summarizeoverlaps biocParallel
9.0 years ago chriad ▴ 10
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5
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2.1k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
9.1 years ago philipp.wahle • 0
4
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3
replies
3.3k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
9.2 years ago ErickF ▴ 40
2
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2
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2.1k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 17 months ago by • 0 • written 9.2 years ago by ▴ 90
2
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9
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2.2k
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SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 9.5 years ago by ★ 6.8k • written 9.5 years ago by ▴ 10
0
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3
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2.0k
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summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
9.5 years ago vedran.franke • 0
2
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7
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3.0k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
9.5 years ago tmartinez • 0
0
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1
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1.3k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
9.6 years ago diogo.camacho.2008 • 0
0
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2
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1.9k
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Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
0
votes
1
reply
2.0k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by • 0
4
votes
11
replies
3.1k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by ▴ 10
1
vote
4
replies
1.9k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 570
2
votes
4
replies
2.9k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
9.7 years ago bioprog • 0
1
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2
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1.3k
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 9.7 years ago by ★ 13k • written 9.7 years ago by • 0
2
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5
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3.5k
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GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by ▴ 30
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3
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1.8k
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Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
10.0 years ago • updated 9.9 years ago Pau Marc Muñoz Torres ▴ 20
8
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9
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6.7k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 10.2 years ago by • 0 • written 10.2 years ago by ★ 1.5k
0
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20
replies
7.7k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 10.2 years ago by ▴ 90 • written 10.2 years ago by ▴ 10
11
votes
8
replies
5.2k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 10
0
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1
reply
1.9k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 10.5 years ago by ★ 6.8k • written 10.5 years ago by 6.7k
6
votes
14
replies
7.0k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.7 years ago by 53k • written 10.7 years ago by • 0
0
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3
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2.8k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 10.8 years ago by ★ 8.2k • written 10.8 years ago by ▴ 20
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Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
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