Showing : summarizeoverlaps • reset
11
votes
8
replies
4.4k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
8
votes
9
replies
6.0k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.8 years ago by • 0 • written 8.8 years ago by ★ 1.5k
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
4
votes
3
replies
1.0k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 10
4
votes
11
replies
2.3k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by ▴ 10
4
votes
3
replies
2.9k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
7.8 years ago ErickF ▴ 40
3
votes
3
replies
1.8k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
2
votes
4
replies
2.5k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.3 years ago bioprog • 0
2
votes
9
replies
1.6k
views
SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 25 days ago by • 0 • written 7.9 years ago by ▴ 90
2
votes
7
replies
2.0k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
8.2 years ago tmartinez • 0
2
votes
6
replies
1.4k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
2
votes
2
replies
1.1k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 6.0 years ago by ★ 6.8k • written 6.0 years ago by ★ 7.9k
2
votes
2
replies
883
views
question about summrizeOverlaps
summarizeoverlaps
updated 7.2 years ago by 25k • written 7.2 years ago by ★ 1.3k
2
votes
5
replies
2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 30
2
votes
3
replies
2.1k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 7.5 years ago by ★ 1.7k • written 7.5 years ago by • 0
1
vote
4
replies
1.5k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 570
1
vote
2
replies
1.1k
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 8.4 years ago by ★ 13k • written 8.4 years ago by • 0
1
vote
1
reply
2.2k
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
7.6 years ago chriad ▴ 10
1
vote
1
reply
1.3k
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 10
1
vote
0
replies
1.2k
views
generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readGAlignmentPairs
7.1 years ago teresati ▴ 10
1
vote
2
replies
1.1k
views
Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 10
1
vote
1
reply
2.0k
views
Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 6.5 years ago by ▴ 160 • written 6.5 years ago by ▴ 10
1
vote
1
reply
1.9k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 6.2 years ago by 65k • written 6.2 years ago by • 0
1
vote
6
replies
1.5k
views
deconvole counts per feature from summerizedOverlaps with GRangesLists
summarizeoverlaps rangedsummarizedexperiment grangeslist summarizedexperiment
6.1 years ago cosmin • 0
1
vote
9
replies
1.3k
views
Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 5.2 years ago by 65k • written 5.2 years ago by ▴ 10
0
votes
20
replies
6.1k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 10
0
votes
0
replies
962
views
Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
6.1 years ago A ▴ 40
0
votes
1
reply
1.0k
views
counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 6.0 years ago by ★ 6.8k • written 6.1 years ago by • 0
0
votes
1
reply
1.6k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by 6.7k
0
votes
0
replies
808
views
Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
3.8 years ago dequattro.concetta ▴ 10
0
votes
9
replies
1.4k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
0
votes
2
replies
994
views
Minimum overlap for reads to be counted in summarizeoverlaps
summarizeoverlaps R
updated 6.2 years ago by ★ 6.8k • written 6.2 years ago by • 0
0
votes
3
replies
2.4k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 9.5 years ago by ★ 8.2k • written 9.5 years ago by ▴ 20
0
votes
3
replies
1.7k
views
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
8.1 years ago vedran.franke • 0
0
votes
1
reply
1.1k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
8.2 years ago diogo.camacho.2008 • 0
0
votes
2
replies
1.6k
views
Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
0
votes
1
reply
1.5k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 8.2 years ago by ★ 6.8k • written 8.2 years ago by • 0
0
votes
5
replies
1.7k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
7.7 years ago philipp.wahle • 0
0
votes
0
replies
1.2k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 10
0
votes
1
reply
1.1k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 40
0
votes
3
replies
1.4k
views
Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
8.6 years ago Pau Marc Muñoz Torres ▴ 20
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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Comment: biomaRt : No lock file for BiocFileCache
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