Showing : summarizeoverlaps • reset
0
votes
20
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6.1k
views
SummarizeOverlaps in R
summarizeoverlaps Bam rstudio
updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 10
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.4 years ago by 50k • written 9.4 years ago by • 0
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
2
votes
9
replies
1.7k
views
SummarizeOverlaps without reference genome ?
summarizeoverlaps
updated 8.1 years ago by ★ 6.8k • written 8.1 years ago by ▴ 10
0
votes
9
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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
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 8.9 years ago by ★ 1.5k
1
vote
9
replies
1.4k
views
Memory issues in summarizeOverlaps funtion
memory summarizeOverlaps
updated 5.2 years ago by 65k • written 5.2 years ago by ▴ 10
11
votes
8
replies
4.5k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
2
votes
7
replies
2.1k
views
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
8.2 years ago tmartinez • 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
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
5
replies
2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by ▴ 30
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
2
votes
4
replies
2.5k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps RNAseq annotation counts
8.3 years ago bioprog • 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
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
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
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
1.4k
views
Default Rapidr invalid class “SummarizedExperiment”
software error RAPIDR summarizeoverlaps R
8.6 years ago Pau Marc Muñoz Torres ▴ 20
0
votes
3
replies
1.7k
views
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps
8.2 years ago vedran.franke • 0
4
votes
3
replies
2.9k
views
Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps rnaseq bplapply rangedsummarizedexperiment read counting
7.9 years ago • updated 7.8 years ago ErickF ▴ 40
4
votes
3
replies
1.0k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 10
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
2
votes
2
replies
888
views
question about summrizeOverlaps
summarizeoverlaps
updated 7.2 years ago by 25k • written 7.2 years ago by ★ 1.3k
0
votes
2
replies
1.0k
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
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 5 weeks ago by • 0 • written 7.9 years ago by ▴ 90
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
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 6.1 years ago by ★ 6.8k • written 6.1 years ago by ★ 7.9k
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
0
votes
1
reply
1.1k
views
counting reads with muliple hits with SummarizeOverlaps
R seq ngs summarizeoverlaps
updated 6.1 years ago by ★ 6.8k • written 6.1 years ago by • 0
0
votes
1
reply
1.1k
views
No reads with summarizeOverlaps
summarizeoverlaps rnaseq
8.2 years ago diogo.camacho.2008 • 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
7.7 years ago chriad ▴ 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
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
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 6.3 years ago by 65k • written 6.3 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
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
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
0
replies
818
views
Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
3.8 years ago dequattro.concetta ▴ 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
0
votes
0
replies
968
views
Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
6.1 years ago A ▴ 40
42 results • Page 1 of 1
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Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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