Showing : summarizeOverlaps • reset
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
4.5 years ago dequattro.concetta ▴ 10
4
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3
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1.3k
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Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 4.7 years ago by 67k • written 4.7 years ago by ▴ 10
0
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9
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1.7k
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summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
1
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9
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1.6k
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Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 5.9 years ago by 67k • written 5.9 years ago by ▴ 10
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1
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1.2k
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counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 6.7 years ago by ★ 6.8k • written 6.7 years ago by • 0
2
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2
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1.3k
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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 6.7 years ago by ★ 6.8k • written 6.7 years ago by ★ 7.9k
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1.1k
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
6.7 years ago A ▴ 40
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0
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1.3k
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large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 10
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6
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1.8k
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deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.8 years ago cosmin • 0
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2
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1.2k
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Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps R
updated 6.8 years ago by ★ 6.8k • written 6.8 years ago by • 0
1
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1
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2.1k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 6.9 years ago by 67k • written 6.9 years ago by • 0
1
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1
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2.4k
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Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 7.1 years ago by ▴ 160 • written 7.1 years ago by ▴ 10
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2
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1.2k
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Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 10
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1.3k
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readGAlignmentPairs
7.7 years ago teresati ▴ 10
1
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1
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1.5k
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summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 10
3
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3
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2.0k
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Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 10
2
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2
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1.0k
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question about summrizeOverlaps
summarizeoverlaps
updated 7.8 years ago by 25k • written 7.8 years ago by ★ 1.3k
0
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1
reply
1.3k
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GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 7.8 years ago by 67k • written 7.8 years ago by ▴ 40
2
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6
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1.7k
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DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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3
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2.4k
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SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 8.1 years ago by ★ 1.7k • written 8.1 years ago by • 0
1
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1
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2.3k
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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
8.3 years ago chriad ▴ 10
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5
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1.9k
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summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
8.3 years ago philipp.wahle • 0
4
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3
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3.1k
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Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
8.5 years ago ErickF ▴ 40
2
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2
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1.8k
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Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 8 months ago by • 0 • written 8.5 years ago by ▴ 90
2
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9
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1.9k
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SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by ▴ 10
0
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3
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1.9k
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summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
8.8 years ago vedran.franke • 0
2
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7
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2.5k
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Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
8.8 years ago tmartinez • 0
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1
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1.2k
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No reads with summarizeOverlaps
summarizeoverlaps rnaseq
8.8 years ago diogo.camacho.2008 • 0
0
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2
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1.8k
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Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
0
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1
reply
1.8k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by • 0
4
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11
replies
2.7k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ▴ 10
1
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4
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1.7k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 570
2
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4
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2.7k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.9 years ago bioprog • 0
1
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2
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1.2k
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Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 9.0 years ago by ★ 13k • written 9.0 years ago by • 0
2
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5
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3.2k
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GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 30
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3
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1.6k
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Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
9.3 years ago • updated 9.2 years ago Pau Marc Muñoz Torres ▴ 20
8
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9
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6.3k
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could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 9.4 years ago by • 0 • written 9.5 years ago by ★ 1.5k
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20
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6.9k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 9.4 years ago by ▴ 90 • written 9.4 years ago by ▴ 10
11
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8
replies
4.8k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 10
0
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1
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1.8k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 9.8 years ago by ★ 6.8k • written 9.8 years ago by 6.7k
6
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14
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6.4k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.0 years ago by 52k • written 10.0 years ago by • 0
0
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3
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2.6k
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Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 10.1 years ago by ★ 8.2k • written 10.1 years ago by ▴ 20
42 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
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Scholar to James W. MacDonald 67k
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