Showing : summarizeOverlaps • reset
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
4.3 years ago dequattro.concetta ▴ 10
4
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3
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1.2k
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Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 4.6 years ago by 67k • written 4.6 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 5.4 years ago by 25k • written 5.4 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 5.8 years ago by 67k • written 5.8 years ago by ▴ 10
0
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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 6.6 years ago by ★ 6.8k • written 6.6 years ago by • 0
2
votes
2
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1.2k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 6.6 years ago by ★ 6.8k • written 6.6 years ago by ★ 7.9k
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0
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1.1k
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
6.6 years ago A ▴ 40
0
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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 6.6 years ago by 25k • written 6.6 years ago by ▴ 10
1
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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
6.6 years ago cosmin • 0
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 6.7 years ago by ★ 6.8k • written 6.7 years ago by • 0
1
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1
reply
2.1k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 6.8 years ago by 67k • written 6.8 years ago by • 0
1
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1
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2.3k
views
Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts
updated 7.0 years ago by ▴ 160 • written 7.0 years ago by ▴ 10
1
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2
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1.2k
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Problems with summarizeOverlaps
bioconductor rnaseq summarizeoverlaps
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 10
1
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0
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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
7.6 years ago teresati ▴ 10
1
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1
reply
1.5k
views
summarizeOverlaps counting exons and 5UTR reads
summarizeoverlaps rnaseq
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
3
votes
3
replies
1.9k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
2
votes
2
replies
986
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question about summrizeOverlaps
summarizeoverlaps
updated 7.7 years ago by 25k • written 7.7 years ago by ★ 1.3k
0
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1
reply
1.3k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 7.7 years ago by 67k • written 7.7 years ago by ▴ 40
2
votes
6
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1.6k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 7.9 years ago by 42k • written 7.9 years ago by • 0
2
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3
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2.3k
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SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 8.0 years ago by ★ 1.7k • written 8.0 years ago by • 0
1
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1
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2.3k
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
8.2 years ago chriad ▴ 10
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5
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1.9k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
8.2 years ago philipp.wahle • 0
4
votes
3
replies
3.1k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
8.4 years ago ErickF ▴ 40
2
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2
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1.8k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 7 months ago by • 0 • written 8.4 years ago by ▴ 90
2
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9
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1.9k
views
SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 8.6 years ago by ★ 6.8k • written 8.6 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
8.7 years ago vedran.franke • 0
2
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7
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2.4k
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Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
8.7 years ago tmartinez • 0
0
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1
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1.2k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
8.7 years ago diogo.camacho.2008 • 0
0
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2
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1.7k
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Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 8.7 years ago by 42k • written 8.7 years ago by • 0
0
votes
1
reply
1.7k
views
Using summarizeOverlaps for bacterial genomes
summarizeoverlaps bacteria e coli unique reads
updated 8.7 years ago by ★ 6.8k • written 8.7 years ago by • 0
4
votes
11
replies
2.6k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps summarizedexperiment count matrix low counts rna-seq
updated 8.7 years ago by ★ 6.8k • written 8.8 years ago by ▴ 10
1
vote
4
replies
1.6k
views
summarizeOverlaps error with hg38
summarizeOverlaps
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 570
2
votes
4
replies
2.7k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.8 years ago bioprog • 0
1
vote
2
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1.2k
views
Feasibility of adapting iRanges to count concomittant drug therapy
summarizeoverlaps
updated 8.9 years ago by ★ 13k • written 8.9 years ago by • 0
2
votes
5
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3.1k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by ▴ 30
0
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3
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1.6k
views
Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
9.1 years ago Pau Marc Muñoz Torres ▴ 20
8
votes
9
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6.2k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 9.3 years ago by • 0 • written 9.4 years ago by ★ 1.5k
0
votes
20
replies
6.8k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 9.3 years ago by ▴ 90 • written 9.3 years ago by ▴ 10
11
votes
8
replies
4.8k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.6 years ago by 16k • written 9.6 years ago by ▴ 10
0
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1
reply
1.8k
views
tuning memory consumption of summarizeOverlaps?
rna-seq summarizeoverlaps
updated 9.6 years ago by ★ 6.8k • written 9.6 years ago by 6.7k
6
votes
14
replies
6.3k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.9 years ago by 51k • written 9.9 years ago by • 0
0
votes
3
replies
2.6k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 10.0 years ago by ★ 8.2k • written 10.0 years ago by ▴ 20
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
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Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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