Showing : summarizeOverlaps • reset
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
22 months ago dequattro.concetta ▴ 10
4
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3
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473
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 2.1 years ago by 59k • written 2.1 years ago by ▴ 10
0
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9
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687
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summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 3.0 years ago by 25k • written 3.0 years ago by • 0
1
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9
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678
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Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 3.3 years ago by 59k • written 3.3 years ago by ▴ 10
0
votes
1
reply
592
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counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 4.1 years ago by ★ 6.7k • written 4.1 years ago by • 0
2
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2
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544
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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 4.1 years ago by ★ 6.7k • written 4.1 years ago by 7.8k
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517
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
4.2 years ago A ▴ 40
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0
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639
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large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 10
1
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6
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772
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deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
4.2 years ago cosmin • 0
0
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2
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481
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Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps R
updated 4.3 years ago by ★ 6.7k • written 4.3 years ago by • 0
1
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1
reply
975
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 4.3 years ago by 59k • written 4.3 years ago by • 0
1
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1
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1.2k
views
Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 4.6 years ago by ▴ 160 • written 4.6 years ago by ▴ 10
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2
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719
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Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 5.0 years ago by 25k • written 5.0 years ago by ▴ 10
1
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0
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819
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readGAlignmentPairs
5.1 years ago teresati ▴ 10
1
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1
reply
835
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 5.2 years ago by 15k • written 5.2 years ago by ▴ 10
3
votes
3
replies
1.1k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 5.2 years ago by 15k • written 5.2 years ago by ▴ 10
2
votes
2
replies
532
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question about summrizeOverlaps
summarizeoverlaps
updated 5.3 years ago by 25k • written 5.3 years ago by ★ 1.3k
0
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1
reply
744
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GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 5.3 years ago by 59k • written 5.3 years ago by ▴ 40
2
votes
6
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953
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 5.4 years ago by 37k • written 5.5 years ago by • 0
2
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3
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1.4k
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SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 5.5 years ago by ★ 1.7k • written 5.5 years ago by • 0
1
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1
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1.7k
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
5.7 years ago chriad ▴ 10
0
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5
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1.2k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
5.8 years ago philipp.wahle • 0
4
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3
replies
2.3k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
5.9 years ago ErickF ▴ 40
2
votes
2
replies
1.0k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
5.9 years ago Jon Manning ▴ 90
2
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9
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1.1k
views
SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 6.2 years ago by ★ 6.7k • written 6.2 years ago by ▴ 10
0
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3
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1.3k
views
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
6.2 years ago vedran.franke • 0
2
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7
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1.2k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
6.2 years ago tmartinez • 0
0
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1
reply
786
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
6.3 years ago diogo.camacho.2008 • 0
0
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2
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1.0k
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Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 6.3 years ago by 37k • written 6.3 years ago by • 0
0
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1
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1.0k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 6.3 years ago by ★ 6.7k • written 6.3 years ago by • 0
4
votes
11
replies
1.5k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 6.3 years ago by ★ 6.7k • written 6.3 years ago by ▴ 10
1
vote
4
replies
974
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 6.3 years ago by 15k • written 6.3 years ago by ▴ 570
2
votes
4
replies
1.9k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
6.4 years ago bioprog • 0
1
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2
replies
688
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 6.4 years ago by 13k • written 6.4 years ago by • 0
2
votes
5
replies
2.1k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 6.5 years ago by ★ 6.7k • written 6.5 years ago by ▴ 30
0
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3
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989
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Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
6.7 years ago • updated 6.6 years ago Pau Marc Muñoz Torres ▴ 20
8
votes
9
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5.1k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 6.9 years ago by • 0 • written 6.9 years ago by ★ 1.5k
0
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20
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4.5k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by ▴ 10
11
votes
8
replies
3.4k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 7.2 years ago by 15k • written 7.2 years ago by ▴ 10
0
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1
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1.2k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 7.2 years ago by ★ 6.7k • written 7.2 years ago by 6.6k
6
votes
14
replies
4.6k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 7.4 years ago by 45k • written 7.4 years ago by • 0
0
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3
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1.7k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 7.5 years ago by ★ 8.2k • written 7.5 years ago by ▴ 20
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Comment: error with: .make_splicings <- function(exons, cds, stop_codons=NULL) by Hervé Pagès 15k
And also please don't ignore these warnings: 1: package ‘GenomicFeatures’ was built under R version 4.1.1 2: package ‘BiocGenerics’ was b…
Comment: broken chain import in liftOver by Marcel Ramos 570
You could also try using one of the chain files in `AnnotationHub`, which gets auto-cached: ```r library(AnnotationHub) query(ah <- Annot…
Answer: paired analysis : return data matrix with indvidual/subject effects eliminated. by James W. MacDonald 59k
See `removeBatchEffect` in the `limma` package.
Comment: GDCdownload Directory Problem :( by Marcel Ramos 570
FWIW, `TCGAutils` is not a related package.
Comment: help please！ by 1051444231 • 0
I have updated Rtools
Votes
Answer: broken chain import in liftOver
Answer: toGRanges help!
Answer: toGRanges help!
Comment: CPM after RUVseq
A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
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